rs1806851

Variant names:

• chr1-145926584-G-A
• rs1806851
• NM_005105.5:c.240C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-145926584-G-A
• chr1-145926584-G-T

Variant summary

Our verdict is Benign. The variant received -19 ACMG points: 0P and 19B. BP4_Moderate BP6_Very_Strong BP7 BS1 BS2

The NM_005105.5(RBM8A):​c.240C>T​(p.Val80Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00082 in 1,614,014 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.0044 (6 hom., cov: 31)
  • Exomes 𝑓: 0.00044 (6 hom.)
• Consequence: RBM8A NM_005105.5 synonymous
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts B:3
• Conservation: PhyloP100: -0.375

Genes affected

RBM8A (HGNC:9905): (RNA binding motif protein 8A) This gene encodes a protein with a conserved RNA-binding motif. The protein is found predominantly in the nucleus, although it is also present in the cytoplasm. It is preferentially associated with mRNAs produced by splicing, including both nuclear mRNAs and newly exported cytoplasmic mRNAs. It is thought that the protein remains associated with spliced mRNAs as a tag to indicate where introns had been present, thus coupling pre- and post-mRNA splicing events. Previously, it was thought that two genes encode this protein, RBM8A and RBM8B; it is now thought that the RBM8B locus is a pseudogene. There are two alternate translation start codons with this gene, which result in two forms of the protein. An allele mutation and a low-frequency noncoding single-nucleotide polymorphism (SNP) in this gene cause thrombocytopenia-absent radius (TAR) syndrome. [provided by RefSeq, Jul 2013]

ENSG00000289565 (HGNC:):

LIX1L-AS1 (HGNC:41210): (LIX1L antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -19 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.41).
• BP6: Variant 1-145926584-G-A is Benign according to our data. Variant chr1-145926584-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 436517.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP7: Synonymous conserved (PhyloP=-0.375 with no splicing effect.
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00444 (676/152134) while in subpopulation AFR AF = 0.0154 (639/41474). AF 95% confidence interval is 0.0144. There are 6 homozygotes in GnomAd4. There are 316 alleles in the male GnomAd4 subpopulation. Median coverage is 31. This position FAILED quality control check.
• BS2: High Homozygotes in GnomAd4 at 6 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RBM8A	NM_005105.5	c.240C>T	p.Val80Val	synonymous_variant	Exon 4 of 6	ENST00000583313.7	NP_005096.1
LIX1L-AS1	NR_147182.1	n.-247G>A		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RBM8A	ENST00000583313.7	c.240C>T	p.Val80Val	synonymous_variant	Exon 4 of 6	1	NM_005105.5	ENSP00000463058.2
ENSG00000289565	ENST00000632040.1	n.33C>T		non_coding_transcript_exon_variant	Exon 1 of 5	2		ENSP00000488887.1

Frequencies

GnomAD3 genomes AF: 0.00445 AC: 676 AN: 152016 Hom.: 6 Cov.: 31

Gnomad AFR AF: 0.0154

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00203

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000147

Gnomad OTH AF: 0.00239

GnomAD2 exomes AF: 0.00121 AC: 304 AN: 251418 AF XY: 0.000787

Gnomad AFR exome AF: 0.0172

Gnomad AMR exome AF: 0.000492

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.000489

GnomAD4 exome AF: 0.000443 AC: 647 AN: 1461880 Hom.: 6 Cov.: 31 AF XY: 0.000391 AC XY: 284 AN XY: 727242

Gnomad4 AFR exome AF: 0.0161 AC: 540 AN: 33480

Gnomad4 AMR exome AF: 0.000738 AC: 33 AN: 44722

Gnomad4 ASJ exome AF: 0.00 AC: 0 AN: 26136

Gnomad4 EAS exome AF: 0.00 AC: 0 AN: 39700

Gnomad4 SAS exome AF: 0.0000812 AC: 7 AN: 86256

Gnomad4 FIN exome AF: 0.00 AC: 0 AN: 53420

Gnomad4 NFE exome AF: 0.00000270 AC: 3 AN: 1112004

Gnomad4 Remaining exome AF: 0.00103 AC: 62 AN: 60396

GnomAD4 genome AF: 0.00444 AC: 676 AN: 152134 Hom.: 6 Cov.: 31 AF XY: 0.00425 AC XY: 316 AN XY: 74396

Gnomad4 AFR AF: 0.0154 AC: 0.0154072 AN: 0.0154072

Gnomad4 AMR AF: 0.00196 AC: 0.00196412 AN: 0.00196412

Gnomad4 ASJ AF: 0.00 AC: 0 AN: 0

Gnomad4 EAS AF: 0.00 AC: 0 AN: 0

Gnomad4 SAS AF: 0.000208 AC: 0.000207555 AN: 0.000207555

Gnomad4 FIN AF: 0.00 AC: 0 AN: 0

Gnomad4 NFE AF: 0.0000147 AC: 0.0000147067 AN: 0.0000147067

Gnomad4 OTH AF: 0.00237 AC: 0.00236742 AN: 0.00236742

Alfa AF: 0.00143 Hom.: 1

Bravo AF: 0.00501

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not specified Benign:1

Sep 30, 2015

Genetic Services Laboratory, University of Chicago

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Radial aplasia-thrombocytopenia syndrome Benign:1

Feb 02, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided Benign:1

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.41
CADD	Benign	8.6
DANN	Benign	0.92
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1806851; hg19: chr1-145508509;