15-61275924-C-T

Variant names:

• chr15-61275924-C-T
• rs7175875

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.921 in 152,246 control chromosomes in the GnomAD database, including 65,307 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 (65307 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0880
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.46).
• BA1: GnomAd4 highest subpopulation (NFE) 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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.922 AC: 140200 AN: 152128 Hom.: 65291 Cov.: 31

Gnomad AFR AF: 0.789

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.894

Gnomad ASJ AF: 0.999

Gnomad EAS AF: 0.821

Gnomad SAS AF: 0.975

Gnomad FIN AF: 0.978

Gnomad MID AF: 0.991

Gnomad NFE AF: 0.998

Gnomad OTH AF: 0.928

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

GnomAD4 genome AF: 0.921 AC: 140262 AN: 152246 Hom.: 65307 Cov.: 31 AF XY: 0.920 AC XY: 68499 AN XY: 74438

African (AFR) AF: 0.789 AC: 32738 AN: 41516

American (AMR) AF: 0.894 AC: 13662 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.999 AC: 3468 AN: 3472

East Asian (EAS) AF: 0.820 AC: 4239 AN: 5168

South Asian (SAS) AF: 0.975 AC: 4708 AN: 4830

European-Finnish (FIN) AF: 0.978 AC: 10379 AN: 10616

Middle Eastern (MID) AF: 0.993 AC: 292 AN: 294

European-Non Finnish (NFE) AF: 0.998 AC: 67912 AN: 68038

Other (OTH) AF: 0.925 AC: 1952 AN: 2110

Alfa AF: 0.919 Hom.: 12183

Bravo AF: 0.908

Asia WGS AF: 0.880 AC: 3063 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.46
CADD	Benign	3.3
DANN	Benign	0.48
PhyloP100		-0.088

Splicing

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

Other links and lift over

dbSNP: rs7175875; hg19: chr15-61568123;