7-150902117-A-G

Variant names:

• chr7-150902117-A-G
• rs10216051

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 0.477 in 151,820 control chromosomes in the GnomAD database, including 18,644 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 0.48 (18644 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.549
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.713 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: 0.477 AC: 72374 AN: 151702 Hom.: 18604 Cov.: 30

Gnomad AFR AF: 0.642

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.557

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.732

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.417

Gnomad MID AF: 0.395

Gnomad NFE AF: 0.360

Gnomad OTH AF: 0.465

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

GnomAD4 genome AF: 0.477 AC: 72491 AN: 151820 Hom.: 18644 Cov.: 30 AF XY: 0.482 AC XY: 35735 AN XY: 74182

African (AFR) AF: 0.642 AC: 26566 AN: 41396

American (AMR) AF: 0.558 AC: 8513 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.469 AC: 1626 AN: 3468

East Asian (EAS) AF: 0.732 AC: 3763 AN: 5140

South Asian (SAS) AF: 0.360 AC: 1728 AN: 4804

European-Finnish (FIN) AF: 0.417 AC: 4388 AN: 10530

Middle Eastern (MID) AF: 0.404 AC: 118 AN: 292

European-Non Finnish (NFE) AF: 0.360 AC: 24472 AN: 67912

Other (OTH) AF: 0.468 AC: 986 AN: 2108

Alfa AF: 0.406 Hom.: 24689

Bravo AF: 0.503

Asia WGS AF: 0.539 AC: 1872 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.2
DANN	Benign	0.75
PhyloP100		0.55

Splicing

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

Other links and lift over

dbSNP: rs10216051; hg19: chr7-150599205;