rs615960

Variant names:

• chr3-40745183-G-A
• rs615960
• ENST00000665970.1:n.57+25268G>A

Your query was ambiguous. Multiple possible variants found:

• chr3-40745183-G-A
• chr3-40745183-G-C
• chr3-40745183-G-T

Variant summary

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

The ENST00000665970.1(ENSG00000231873):​n.57+25268G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.916 in 152,220 control chromosomes in the GnomAD database, including 65,044 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 0.92 (65044 hom., cov: 32)
• Consequence: ENSG00000231873 ENST00000665970.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.468
• Publications: 0 publications found

Genes affected

ENSG00000231873 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.992 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000665970.1. 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
	ENSG00000231873	ENST00000665970.1		n.57+25268G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.916 AC: 139334 AN: 152102 Hom.: 65018 Cov.: 32

Gnomad AFR AF: 0.713

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.962

Gnomad ASJ AF: 0.991

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.998

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.959

Gnomad NFE AF: 0.998

Gnomad OTH AF: 0.932

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

GnomAD4 genome AF: 0.916 AC: 139416 AN: 152220 Hom.: 65044 Cov.: 32 AF XY: 0.919 AC XY: 68402 AN XY: 74434

African (AFR) AF: 0.713 AC: 29569 AN: 41466

American (AMR) AF: 0.962 AC: 14723 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.991 AC: 3440 AN: 3470

East Asian (EAS) AF: 1.00 AC: 5186 AN: 5186

South Asian (SAS) AF: 0.998 AC: 4817 AN: 4826

European-Finnish (FIN) AF: 1.00 AC: 10614 AN: 10614

Middle Eastern (MID) AF: 0.956 AC: 281 AN: 294

European-Non Finnish (NFE) AF: 0.998 AC: 67900 AN: 68038

Other (OTH) AF: 0.933 AC: 1974 AN: 2116

Alfa AF: 0.969 Hom.: 201988

Bravo AF: 0.902

Asia WGS AF: 0.980 AC: 3406 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	9.4
DANN	Benign	0.75
PhyloP100		0.47

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: rs615960;

hg19: chr3-40786674;