rs10243511

Variant names:

• chr7-50442571-G-A
• rs10243511

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 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

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;