7-96771733-C-T

Variant names:

• chr7-96771733-C-T
• rs12375086

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.0375 AC: 1556 AN: 41536

American (AMR) AF: 0.0729 AC: 1113 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 500 AN: 3468

East Asian (EAS) AF: 0.0999 AC: 517 AN: 5174

South Asian (SAS) AF: 0.136 AC: 653 AN: 4816

European-Finnish (FIN) AF: 0.0804 AC: 851 AN: 10588

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6872 AN: 67966

Other (OTH) AF: 0.103 AC: 216 AN: 2106

Alfa AF: 0.0941 Hom.: 935

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
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs12375086; hg19: chr7-96401045;