chr15-74764017-G-A

Variant names:

• chr15-74764017-G-A
• rs11631682

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 0.0478 in 152,212 control chromosomes in the GnomAD database, including 251 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 0.048 (251 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0460
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0883 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: 0.0478 AC: 7274 AN: 152094 Hom.: 251 Cov.: 32

Gnomad AFR AF: 0.0909

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.0331

Gnomad ASJ AF: 0.0614

Gnomad EAS AF: 0.0733

Gnomad SAS AF: 0.0854

Gnomad FIN AF: 0.0373

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0216

Gnomad OTH AF: 0.0423

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

GnomAD4 genome AF: 0.0478 AC: 7272 AN: 152212 Hom.: 251 Cov.: 32 AF XY: 0.0492 AC XY: 3665 AN XY: 74446

African (AFR) AF: 0.0907 AC: 3765 AN: 41514

American (AMR) AF: 0.0330 AC: 505 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0614 AC: 213 AN: 3470

East Asian (EAS) AF: 0.0727 AC: 377 AN: 5186

South Asian (SAS) AF: 0.0861 AC: 415 AN: 4818

European-Finnish (FIN) AF: 0.0373 AC: 396 AN: 10604

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0216 AC: 1472 AN: 68010

Other (OTH) AF: 0.0418 AC: 88 AN: 2104

Alfa AF: 0.0332 Hom.: 198

Bravo AF: 0.0479

Asia WGS AF: 0.0700 AC: 241 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.9
DANN	Benign	0.58
PhyloP100		-0.046

Splicing

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

Other links and lift over

dbSNP: rs11631682; hg19: chr15-75056358;