rs6549878

Variant names:

• chr3-28703756-C-A
• rs6549878
• ENST00000635992.1:n.*339+127260C>A

Your query was ambiguous. Multiple possible variants found:

• chr3-28703756-C-A
• chr3-28703756-C-G
• chr3-28703756-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000635992.1(ENSG00000283563):​n.*339+127260C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.928 in 152,264 control chromosomes in the GnomAD database, including 65,687 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 0.93 (65687 hom., cov: 33)
• Consequence: ENSG00000283563 ENST00000635992.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.670
• Publications: 3 publications found

Genes affected

ENSG00000283563 (HGNC:):

RBMS3 (HGNC:13427): (RNA binding motif single stranded interacting protein 3) This gene encodes an RNA-binding protein that belongs to the c-myc gene single-strand binding protein family. These proteins are characterized by the presence of two sets of ribonucleoprotein consensus sequence (RNP-CS) that contain conserved motifs, RNP1 and RNP2, originally described in RNA binding proteins, and required for DNA binding. These proteins have been implicated in such diverse functions as DNA replication, gene transcription, cell cycle progression and apoptosis. The encoded protein was isolated by virtue of its binding to an upstream element of the alpha2(I) collagen promoter. The observation that this protein localizes mostly in the cytoplasm suggests that it may be involved in a cytoplasmic function such as controlling RNA metabolism, rather than transcription. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2010]

LINC00693 (HGNC:44526): (long intergenic non-protein coding RNA 693)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.935 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00693	NR_038840.1	n.323-53002C>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000283563	ENST00000635992.1	n.*339+127260C>A		intron_variant	Intron 6 of 13	5		ENSP00000489994.1

Frequencies

GnomAD3 genomes AF: 0.928 AC: 141242 AN: 152146 Hom.: 65637 Cov.: 33

Gnomad AFR AF: 0.916

Gnomad AMI AF: 0.998

Gnomad AMR AF: 0.944

Gnomad ASJ AF: 0.919

Gnomad EAS AF: 0.846

Gnomad SAS AF: 0.824

Gnomad FIN AF: 0.955

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.941

Gnomad OTH AF: 0.929

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

GnomAD4 genome AF: 0.928 AC: 141349 AN: 152264 Hom.: 65687 Cov.: 33 AF XY: 0.926 AC XY: 68922 AN XY: 74456

African (AFR) AF: 0.916 AC: 38052 AN: 41544

American (AMR) AF: 0.944 AC: 14432 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.919 AC: 3191 AN: 3472

East Asian (EAS) AF: 0.847 AC: 4376 AN: 5168

South Asian (SAS) AF: 0.823 AC: 3980 AN: 4834

European-Finnish (FIN) AF: 0.955 AC: 10133 AN: 10616

Middle Eastern (MID) AF: 0.932 AC: 274 AN: 294

European-Non Finnish (NFE) AF: 0.941 AC: 64048 AN: 68028

Other (OTH) AF: 0.926 AC: 1955 AN: 2112

Alfa AF: 0.938 Hom.: 101370

Bravo AF: 0.930

Asia WGS AF: 0.824 AC: 2865 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.35
DANN	Benign	0.33
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs6549878; hg19: chr3-28745247;