7-76713262-C-G

Position:

• chr7-76713262-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 0.226 in 151,964 control chromosomes in the GnomAD database, including 4,213 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 0.23 (4213 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.213

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34297 AN: 151846 Hom.: 4209 Cov.: 31

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.0168

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.226 AC: 34322 AN: 151964 Hom.: 4213 Cov.: 31 AF XY: 0.226 AC XY: 16755 AN XY: 74258

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.297

Gnomad4 EAS AF: 0.0168

Gnomad4 SAS AF: 0.243

Gnomad4 FIN AF: 0.233

Gnomad4 NFE AF: 0.278

Gnomad4 OTH AF: 0.251

Alfa AF: 0.0865 Hom.: 147

Bravo AF: 0.222

Asia WGS AF: 0.124 AC: 430 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	11
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10488497; hg19: chr7-76342579;