rs7395429

chr11-643348-G-Achr11-643348-G-Cchr11-643348-G-T

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 0.507 in 151,610 control chromosomes in the GnomAD database, including 19,748 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 0.51 (19748 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.124

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.507 AC: 76859 AN: 151494 Hom.: 19726 Cov.: 31

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.498

Gnomad EAS AF: 0.732

Gnomad SAS AF: 0.589

Gnomad FIN AF: 0.482

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.505

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

GnomAD4 genome AF: 0.507 AC: 76929 AN: 151610 Hom.: 19748 Cov.: 31 AF XY: 0.510 AC XY: 37815 AN XY: 74088

Gnomad4 AFR AF: 0.448

Gnomad4 AMR AF: 0.542

Gnomad4 ASJ AF: 0.498

Gnomad4 EAS AF: 0.732

Gnomad4 SAS AF: 0.589

Gnomad4 FIN AF: 0.482

Gnomad4 NFE AF: 0.516

Gnomad4 OTH AF: 0.505

Alfa AF: 0.515 Hom.: 22193

Bravo AF: 0.509

Asia WGS AF: 0.619 AC: 2150 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	2.7
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7395429; hg19: chr11-643348;