rs1891904

Positions:

• chr1-1164939-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007065348.1(LOC124903818):​n.1687C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.879 in 152,120 control chromosomes in the GnomAD database, including 59,314 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.88 (59314 hom., cov: 33)
• Consequence: LOC124903818 XR_007065348.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.455

Genes affected

LOC124903818 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.934 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124903818	XR_007065348.1	n.1687C>A		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.879 AC: 133585 AN: 152002 Hom.: 59263 Cov.: 33

Gnomad AFR AF: 0.821

Gnomad AMI AF: 0.990

Gnomad AMR AF: 0.820

Gnomad ASJ AF: 0.907

Gnomad EAS AF: 0.576

Gnomad SAS AF: 0.882

Gnomad FIN AF: 0.923

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.940

Gnomad OTH AF: 0.873

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.879 AC: 133690 AN: 152120 Hom.: 59314 Cov.: 33 AF XY: 0.875 AC XY: 65065 AN XY: 74372

Gnomad4 AFR AF: 0.821

Gnomad4 AMR AF: 0.820

Gnomad4 ASJ AF: 0.907

Gnomad4 EAS AF: 0.577

Gnomad4 SAS AF: 0.883

Gnomad4 FIN AF: 0.923

Gnomad4 NFE AF: 0.940

Gnomad4 OTH AF: 0.873

Alfa AF: 0.910 Hom.: 9730

Bravo AF: 0.866

Asia WGS AF: 0.718 AC: 2498 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.7
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1891904; hg19: chr1-1100319;