7-50442571-G-A

Position:

• chr7-50442571-G-A

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.460

Gnomad4 AMR AF: 0.717

Gnomad4 ASJ AF: 0.751

Gnomad4 EAS AF: 0.500

Gnomad4 SAS AF: 0.604

Gnomad4 FIN AF: 0.640

Gnomad4 NFE AF: 0.711

Gnomad4 OTH AF: 0.669

Alfa AF: 0.707 Hom.: 36928

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10243511; hg19: chr7-50510269;