rs7762246

Variant names:

• chr6-51234458-T-C
• rs7762246

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 152,178 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

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 (NFE) allele frequency at 95% confidence interval = 0.148 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: 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

Gnomad4 AFR AF: 0.0828

Gnomad4 AMR AF: 0.127

Gnomad4 ASJ AF: 0.201

Gnomad4 EAS AF: 0.000773

Gnomad4 SAS AF: 0.0979

Gnomad4 FIN AF: 0.0861

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.152

Alfa AF: 0.151 Hom.: 3141

Bravo AF: 0.119

Asia WGS AF: 0.0440 AC: 157 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7762246; hg19: chr6-51099256;