chr15-61275924-C-T

Variant names:

• chr15-61275924-C-T
• rs7175875

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.789

Gnomad4 AMR AF: 0.894

Gnomad4 ASJ AF: 0.999

Gnomad4 EAS AF: 0.820

Gnomad4 SAS AF: 0.975

Gnomad4 FIN AF: 0.978

Gnomad4 NFE AF: 0.998

Gnomad4 OTH AF: 0.925

Alfa AF: 0.923 Hom.: 11952

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7175875; hg19: chr15-61568123;