15-101617451-T-C

Variant names:

• chr15-101617451-T-C
• rs7168948

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 0.596 in 151,974 control chromosomes in the GnomAD database, including 27,845 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 0.60 (27845 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.293
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.748 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: 0.596 AC: 90445 AN: 151858 Hom.: 27792 Cov.: 32

Gnomad AFR AF: 0.754

Gnomad AMI AF: 0.638

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.387

Gnomad EAS AF: 0.600

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.546

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

GnomAD4 genome AF: 0.596 AC: 90557 AN: 151974 Hom.: 27845 Cov.: 32 AF XY: 0.593 AC XY: 44055 AN XY: 74288

African (AFR) AF: 0.755 AC: 31296 AN: 41464

American (AMR) AF: 0.512 AC: 7822 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.387 AC: 1340 AN: 3462

East Asian (EAS) AF: 0.600 AC: 3084 AN: 5144

South Asian (SAS) AF: 0.495 AC: 2384 AN: 4816

European-Finnish (FIN) AF: 0.518 AC: 5468 AN: 10564

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.549 AC: 37297 AN: 67938

Other (OTH) AF: 0.548 AC: 1158 AN: 2112

Alfa AF: 0.554 Hom.: 10970

Bravo AF: 0.598

Asia WGS AF: 0.588 AC: 2043 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.7
DANN	Benign	0.32
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs7168948; hg19: chr15-102157654;