rs7947143

Variant names:

• chr11-64322950-G-A
• rs7947143

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 0.12 in 152,174 control chromosomes in the GnomAD database, including 1,382 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 0.12 (1382 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0880

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.158 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: 0.120 AC: 18226 AN: 152056 Hom.: 1383 Cov.: 33

Gnomad AFR AF: 0.0431

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.0722

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.120 AC: 18229 AN: 152174 Hom.: 1382 Cov.: 33 AF XY: 0.120 AC XY: 8894 AN XY: 74404

Gnomad4 AFR AF: 0.0430

Gnomad4 AMR AF: 0.130

Gnomad4 ASJ AF: 0.116

Gnomad4 EAS AF: 0.110

Gnomad4 SAS AF: 0.0727

Gnomad4 FIN AF: 0.163

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.156

Alfa AF: 0.137 Hom.: 237

Bravo AF: 0.115

Asia WGS AF: 0.116 AC: 401 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	3.1
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7947143; hg19: chr11-64090422;