chr7-50442571-G-A

Variant names:

• chr7-50442571-G-A
• rs10243511

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 0.628 in 152,102 control chromosomes in the GnomAD database, including 31,051 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 0.63 (31051 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.110
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.706 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: 0.628 AC: 95478 AN: 151982 Hom.: 31038 Cov.: 33

Gnomad AFR AF: 0.460

Gnomad AMI AF: 0.735

Gnomad AMR AF: 0.717

Gnomad ASJ AF: 0.751

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.640

Gnomad MID AF: 0.717

Gnomad NFE AF: 0.711

Gnomad OTH AF: 0.669

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

GnomAD4 genome AF: 0.628 AC: 95528 AN: 152102 Hom.: 31051 Cov.: 33 AF XY: 0.626 AC XY: 46519 AN XY: 74332

African (AFR) AF: 0.460 AC: 19084 AN: 41490

American (AMR) AF: 0.717 AC: 10971 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.751 AC: 2606 AN: 3468

East Asian (EAS) AF: 0.500 AC: 2588 AN: 5178

South Asian (SAS) AF: 0.604 AC: 2909 AN: 4820

European-Finnish (FIN) AF: 0.640 AC: 6751 AN: 10548

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.711 AC: 48324 AN: 67986

Other (OTH) AF: 0.669 AC: 1413 AN: 2112

Alfa AF: 0.695 Hom.: 47240

Bravo AF: 0.627

Asia WGS AF: 0.583 AC: 2030 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.8
DANN	Benign	0.53
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs10243511; hg19: chr7-50510269;