7-76713262-C-G

Variant names:

• chr7-76713262-C-G
• rs10488497

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;