7-95296508-A-G

Position:

• chr7-95296508-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.708 in 152,478 control chromosomes in the GnomAD database, including 38,646 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 0.71 (38554 hom., cov: 33)
  • Exomes 𝑓: 0.67 (92 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.21

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.32).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.779 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: 0.709 AC: 107687 AN: 151950 Hom.: 38543 Cov.: 33

Gnomad AFR AF: 0.630

Gnomad AMI AF: 0.679

Gnomad AMR AF: 0.727

Gnomad ASJ AF: 0.793

Gnomad EAS AF: 0.779

Gnomad SAS AF: 0.800

Gnomad FIN AF: 0.638

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.746

Gnomad OTH AF: 0.745

GnomAD4 exome AF: 0.665 AC: 274 AN: 412 Hom.: 92 AF XY: 0.685 AC XY: 170 AN XY: 248

Gnomad4 FIN exome AF: 0.665

Gnomad4 NFE exome AF: 0.500

Gnomad4 OTH exome AF: 0.750

GnomAD4 genome AF: 0.709 AC: 107743 AN: 152066 Hom.: 38554 Cov.: 33 AF XY: 0.708 AC XY: 52594 AN XY: 74314

Gnomad4 AFR AF: 0.630

Gnomad4 AMR AF: 0.726

Gnomad4 ASJ AF: 0.793

Gnomad4 EAS AF: 0.780

Gnomad4 SAS AF: 0.800

Gnomad4 FIN AF: 0.638

Gnomad4 NFE AF: 0.746

Gnomad4 OTH AF: 0.741

Alfa AF: 0.747 Hom.: 58867

Bravo AF: 0.709

Asia WGS AF: 0.758 AC: 2637 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.32
CADD	Benign	18
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs854548; hg19: chr7-94925820; COSMIC: COSV55931628;