7-91651155-C-T

Variant names:

• chr7-91651155-C-T
• rs12673563

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 0.138 in 152,092 control chromosomes in the GnomAD database, including 1,736 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 0.14 (1736 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0210
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.234 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: 0.138 AC: 20965 AN: 151974 Hom.: 1727 Cov.: 32

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.0732

Gnomad EAS AF: 0.0992

Gnomad SAS AF: 0.0583

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0984

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.138 AC: 20998 AN: 152092 Hom.: 1736 Cov.: 32 AF XY: 0.135 AC XY: 10030 AN XY: 74366

African (AFR) AF: 0.238 AC: 9882 AN: 41474

American (AMR) AF: 0.125 AC: 1907 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0732 AC: 254 AN: 3468

East Asian (EAS) AF: 0.0992 AC: 513 AN: 5172

South Asian (SAS) AF: 0.0579 AC: 279 AN: 4816

European-Finnish (FIN) AF: 0.106 AC: 1123 AN: 10600

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0984 AC: 6690 AN: 67972

Other (OTH) AF: 0.109 AC: 229 AN: 2108

Alfa AF: 0.105 Hom.: 1385

Bravo AF: 0.146

Asia WGS AF: 0.0850 AC: 296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.3
DANN	Benign	0.46
PhyloP100		0.021

Splicing

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

Other links and lift over

dbSNP: rs12673563; hg19: chr7-91280470;