15-74883116-G-C

Variant names:

• chr15-74883116-G-C
• rs7497393

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 0.354 in 152,022 control chromosomes in the GnomAD database, including 12,227 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 0.35 (12227 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.243
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.515 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: 0.354 AC: 53770 AN: 151904 Hom.: 12228 Cov.: 31

Gnomad AFR AF: 0.0973

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.354 AC: 53776 AN: 152022 Hom.: 12227 Cov.: 31 AF XY: 0.342 AC XY: 25438 AN XY: 74284

African (AFR) AF: 0.0970 AC: 4027 AN: 41504

American (AMR) AF: 0.410 AC: 6252 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.395 AC: 1370 AN: 3464

East Asian (EAS) AF: 0.154 AC: 797 AN: 5170

South Asian (SAS) AF: 0.126 AC: 605 AN: 4818

European-Finnish (FIN) AF: 0.402 AC: 4241 AN: 10544

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.519 AC: 35279 AN: 67948

Other (OTH) AF: 0.359 AC: 756 AN: 2106

Alfa AF: 0.266 Hom.: 719

Bravo AF: 0.351

Asia WGS AF: 0.140 AC: 490 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	14
DANN	Benign	0.77
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs7497393; hg19: chr15-75175457;