rs7769051

chr6-132825657-C-Achr6-132825657-C-G

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 0.177 in 152,172 control chromosomes in the GnomAD database, including 3,007 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 0.18 (3007 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0870

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 (AFR) allele frequency at 95% confidence interval = 0.311 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: 0.177 AC: 26840 AN: 152054 Hom.: 2997 Cov.: 32

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.0793

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.177 AC: 26885 AN: 152172 Hom.: 3007 Cov.: 32 AF XY: 0.176 AC XY: 13117 AN XY: 74396

Gnomad4 AFR AF: 0.315

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.138

Gnomad4 EAS AF: 0.0797

Gnomad4 SAS AF: 0.181

Gnomad4 FIN AF: 0.158

Gnomad4 NFE AF: 0.118

Gnomad4 OTH AF: 0.174

Alfa AF: 0.117 Hom.: 1625

Bravo AF: 0.176

Asia WGS AF: 0.182 AC: 634 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	0.36
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7769051; hg19: chr6-133146796;