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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377043	XR_007095886.1	n.57+25268G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000231873	ENST00000665970.1	n.57+25268G>A		intron_variant	Intron 1 of 3

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 v4.3

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

Other links and lift over

dbSNP: rs615960; hg19: chr3-40786674;