rs753628

Variant names:

• chr3-194838744-G-A
• rs753628
• ENST00000837650.1:n.326C>T

Your query was ambiguous. Multiple possible variants found:

• chr3-194838744-G-A
• chr3-194838744-G-C

Variant summary

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

The ENST00000837650.1(ENSG00000308981):​n.326C>T 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 0.506 in 152,016 control chromosomes in the GnomAD database, including 21,735 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 0.51 (21735 hom., cov: 32)
• Consequence: ENSG00000308981 ENST00000837650.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.397
• Publications: 3 publications found

Genes affected

ENSG00000308981 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.759 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000308981	ENST00000837650.1	n.326C>T		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000308981	ENST00000837651.1	n.217C>T		non_coding_transcript_exon_variant	Exon 2 of 3
ENSG00000308981	ENST00000837652.1	n.231C>T		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.506 AC: 76893 AN: 151898 Hom.: 21690 Cov.: 32

Gnomad AFR AF: 0.765

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.643

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.506 AC: 76988 AN: 152016 Hom.: 21735 Cov.: 32 AF XY: 0.506 AC XY: 37577 AN XY: 74318

African (AFR) AF: 0.766 AC: 31760 AN: 41474

American (AMR) AF: 0.506 AC: 7734 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.402 AC: 1394 AN: 3470

East Asian (EAS) AF: 0.643 AC: 3312 AN: 5150

South Asian (SAS) AF: 0.424 AC: 2039 AN: 4810

European-Finnish (FIN) AF: 0.406 AC: 4291 AN: 10562

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.368 AC: 24996 AN: 67954

Other (OTH) AF: 0.452 AC: 953 AN: 2110

Alfa AF: 0.422 Hom.: 26407

Bravo AF: 0.529

Asia WGS AF: 0.529 AC: 1841 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.41
DANN	Benign	0.74
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs753628; hg19: chr3-194559473;