7-96771733-C-T

Position:

• chr7-96771733-C-T

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 0.0814 in 152,132 control chromosomes in the GnomAD database, including 588 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 0.081 (588 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.385

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.127 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: 0.0815 AC: 12383 AN: 152014 Hom.: 588 Cov.: 32

Gnomad AFR AF: 0.0372

Gnomad AMI AF: 0.0749

Gnomad AMR AF: 0.0731

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.0993

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.0804

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.0814 AC: 12383 AN: 152132 Hom.: 588 Cov.: 32 AF XY: 0.0819 AC XY: 6088 AN XY: 74380

Gnomad4 AFR AF: 0.0375

Gnomad4 AMR AF: 0.0729

Gnomad4 ASJ AF: 0.144

Gnomad4 EAS AF: 0.0999

Gnomad4 SAS AF: 0.136

Gnomad4 FIN AF: 0.0804

Gnomad4 NFE AF: 0.101

Gnomad4 OTH AF: 0.103

Alfa AF: 0.0958 Hom.: 732

Bravo AF: 0.0791

Asia WGS AF: 0.105 AC: 364 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	12
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12375086; hg19: chr7-96401045;