rs907931

Variant names:

• chr3-129949941-G-A
• rs907931
• ENST00000785099.1:n.636-3342C>T

Your query was ambiguous. Multiple possible variants found:

• chr3-129949941-G-A
• chr3-129949941-G-C
• chr3-129949941-G-T

Variant summary

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

The ENST00000785099.1(ENSG00000250643):​n.636-3342C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.741 in 152,100 control chromosomes in the GnomAD database, including 42,933 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 0.74 (42933 hom., cov: 31)
• Consequence: ENSG00000250643 ENST00000785099.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.889
• Publications: 6 publications found

Genes affected

ENSG00000250643 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.825 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
ENSG00000250643	ENST00000785099.1	n.636-3342C>T		intron_variant	Intron 4 of 4
ENSG00000250643	ENST00000785100.1	n.487-3342C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.741 AC: 112592 AN: 151982 Hom.: 42899 Cov.: 31

Gnomad AFR AF: 0.554

Gnomad AMI AF: 0.827

Gnomad AMR AF: 0.819

Gnomad ASJ AF: 0.803

Gnomad EAS AF: 0.714

Gnomad SAS AF: 0.818

Gnomad FIN AF: 0.723

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.831

Gnomad OTH AF: 0.764

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

GnomAD4 genome AF: 0.741 AC: 112680 AN: 152100 Hom.: 42933 Cov.: 31 AF XY: 0.739 AC XY: 54908 AN XY: 74344

African (AFR) AF: 0.554 AC: 22957 AN: 41438

American (AMR) AF: 0.820 AC: 12532 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.803 AC: 2789 AN: 3472

East Asian (EAS) AF: 0.715 AC: 3693 AN: 5168

South Asian (SAS) AF: 0.818 AC: 3948 AN: 4826

European-Finnish (FIN) AF: 0.723 AC: 7654 AN: 10584

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.831 AC: 56503 AN: 68004

Other (OTH) AF: 0.765 AC: 1615 AN: 2112

Alfa AF: 0.757 Hom.: 4211

Bravo AF: 0.740

Asia WGS AF: 0.748 AC: 2602 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.23
DANN	Benign	0.49
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs907931; hg19: chr3-129668784;