15-70139434-G-T

Variant names:

• chr15-70139434-G-T
• rs11855650

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 0.394 in 152,052 control chromosomes in the GnomAD database, including 11,857 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 0.39 (11857 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.477 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: 0.394 AC: 59852 AN: 151934 Hom.: 11852 Cov.: 32

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.387

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.360

Gnomad EAS AF: 0.383

Gnomad SAS AF: 0.496

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.373

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

GnomAD4 genome AF: 0.394 AC: 59874 AN: 152052 Hom.: 11857 Cov.: 32 AF XY: 0.397 AC XY: 29537 AN XY: 74340

African (AFR) AF: 0.364 AC: 15095 AN: 41458

American (AMR) AF: 0.441 AC: 6741 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.360 AC: 1246 AN: 3464

East Asian (EAS) AF: 0.383 AC: 1984 AN: 5176

South Asian (SAS) AF: 0.494 AC: 2382 AN: 4826

European-Finnish (FIN) AF: 0.398 AC: 4202 AN: 10554

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.397 AC: 26984 AN: 67970

Other (OTH) AF: 0.374 AC: 790 AN: 2114

Alfa AF: 0.393 Hom.: 52575

Bravo AF: 0.394

Asia WGS AF: 0.424 AC: 1475 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.22
DANN	Benign	0.67
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs11855650; hg19: chr15-70431773;