15-64687092-G-C

Variant names:

• chr15-64687092-G-C
• rs7403751

Variant summary

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

The variant allele was found at a frequency of 0.707 in 152,108 control chromosomes in the GnomAD database, including 41,708 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 0.71 (41708 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0400
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.91 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: 0.707 AC: 107490 AN: 151990 Hom.: 41698 Cov.: 31

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.833

Gnomad AMR AF: 0.847

Gnomad ASJ AF: 0.785

Gnomad EAS AF: 0.932

Gnomad SAS AF: 0.528

Gnomad FIN AF: 0.828

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.850

Gnomad OTH AF: 0.760

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

GnomAD4 genome AF: 0.707 AC: 107518 AN: 152108 Hom.: 41708 Cov.: 31 AF XY: 0.706 AC XY: 52530 AN XY: 74382

African (AFR) AF: 0.370 AC: 15315 AN: 41434

American (AMR) AF: 0.847 AC: 12961 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.785 AC: 2725 AN: 3472

East Asian (EAS) AF: 0.932 AC: 4826 AN: 5178

South Asian (SAS) AF: 0.528 AC: 2542 AN: 4816

European-Finnish (FIN) AF: 0.828 AC: 8770 AN: 10592

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.850 AC: 57774 AN: 68006

Other (OTH) AF: 0.764 AC: 1613 AN: 2112

Alfa AF: 0.771 Hom.: 5650

Bravo AF: 0.700

Asia WGS AF: 0.730 AC: 2540 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.6
DANN	Benign	0.77
PhyloP100		-0.040

Splicing

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

Other links and lift over

dbSNP: rs7403751; hg19: chr15-64979291;