rs7762246

Variant names:

• chr6-51234458-T-C
• rs7762246

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.12 in 152,178 control chromosomes in the GnomAD database, including 1,277 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 (1277 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.204
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.148 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18196 AN: 152060 Hom.: 1276 Cov.: 32

Gnomad AFR AF: 0.0827

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.000771

Gnomad SAS AF: 0.0974

Gnomad FIN AF: 0.0861

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.120 AC: 18204 AN: 152178 Hom.: 1277 Cov.: 32 AF XY: 0.115 AC XY: 8570 AN XY: 74394

African (AFR) AF: 0.0828 AC: 3438 AN: 41536

American (AMR) AF: 0.127 AC: 1943 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 697 AN: 3464

East Asian (EAS) AF: 0.000773 AC: 4 AN: 5174

South Asian (SAS) AF: 0.0979 AC: 473 AN: 4830

European-Finnish (FIN) AF: 0.0861 AC: 914 AN: 10618

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10215 AN: 67992

Other (OTH) AF: 0.152 AC: 322 AN: 2114

Alfa AF: 0.143 Hom.: 4822

Bravo AF: 0.119

Asia WGS AF: 0.0440 AC: 157 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.5
DANN	Benign	0.70
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs7762246; hg19: chr6-51099256;