7-132093689-C-T

Variant names:

• chr7-132093689-C-T
• rs10954357

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 0.311 in 151,978 control chromosomes in the GnomAD database, including 7,819 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 0.31 (7819 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.387 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.311 AC: 47172 AN: 151858 Hom.: 7800 Cov.: 33

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.271

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.311 AC: 47239 AN: 151978 Hom.: 7819 Cov.: 33 AF XY: 0.309 AC XY: 22948 AN XY: 74300

African (AFR) AF: 0.392 AC: 16230 AN: 41448

American (AMR) AF: 0.283 AC: 4327 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 786 AN: 3466

East Asian (EAS) AF: 0.269 AC: 1392 AN: 5172

South Asian (SAS) AF: 0.393 AC: 1897 AN: 4822

European-Finnish (FIN) AF: 0.202 AC: 2133 AN: 10550

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.286 AC: 19446 AN: 67932

Other (OTH) AF: 0.320 AC: 675 AN: 2110

Alfa AF: 0.265 Hom.: 2885

Bravo AF: 0.315

Asia WGS AF: 0.364 AC: 1267 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.2
DANN	Benign	0.36
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs10954357; hg19: chr7-131778448;