rs931913

Variant names:

• chr3-36801658-G-A
• rs931913
• ENST00000753312.1:n.81+10620C>T

Variant summary

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

The ENST00000753312.1(ENSG00000292977):​n.81+10620C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 152,126 control chromosomes in the GnomAD database, including 7,617 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 0.31 (7617 hom., cov: 33)
• Consequence: ENSG00000292977 ENST00000753312.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.60
• Publications: 9 publications found

Genes affected

ENSG00000292977 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000753312.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000292977	ENST00000753312.1		n.81+10620C>T		intron	N/A
	ENSG00000292977	ENST00000753313.1		n.79+10620C>T		intron	N/A
	ENSG00000292977	ENST00000753314.1		n.76+10620C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46901 AN: 152008 Hom.: 7609 Cov.: 33

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.0609

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.309 AC: 46939 AN: 152126 Hom.: 7617 Cov.: 33 AF XY: 0.304 AC XY: 22640 AN XY: 74366

African (AFR) AF: 0.272 AC: 11282 AN: 41482

American (AMR) AF: 0.335 AC: 5119 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 983 AN: 3468

East Asian (EAS) AF: 0.0608 AC: 316 AN: 5194

South Asian (SAS) AF: 0.283 AC: 1364 AN: 4820

European-Finnish (FIN) AF: 0.299 AC: 3165 AN: 10570

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.348 AC: 23667 AN: 67980

Other (OTH) AF: 0.304 AC: 644 AN: 2116

Alfa AF: 0.332 Hom.: 17183

Bravo AF: 0.306

Asia WGS AF: 0.193 AC: 673 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	11
DANN	Benign	0.76
PhyloP100		1.6

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs931913;

hg19: chr3-36843149;