7-52157703-T-C

Variant names:

• chr7-52157703-T-C
• rs11238181

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 0.258 in 150,666 control chromosomes in the GnomAD database, including 5,405 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 0.26 (5405 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.677
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.434 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: 0.259 AC: 38920 AN: 150546 Hom.: 5410 Cov.: 29

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.258 AC: 38927 AN: 150666 Hom.: 5405 Cov.: 29 AF XY: 0.267 AC XY: 19651 AN XY: 73470

African (AFR) AF: 0.163 AC: 6706 AN: 41078

American (AMR) AF: 0.285 AC: 4311 AN: 15102

Ashkenazi Jewish (ASJ) AF: 0.345 AC: 1193 AN: 3456

East Asian (EAS) AF: 0.449 AC: 2229 AN: 4960

South Asian (SAS) AF: 0.417 AC: 1987 AN: 4770

European-Finnish (FIN) AF: 0.359 AC: 3670 AN: 10220

Middle Eastern (MID) AF: 0.240 AC: 70 AN: 292

European-Non Finnish (NFE) AF: 0.265 AC: 17972 AN: 67790

Other (OTH) AF: 0.259 AC: 541 AN: 2090

Alfa AF: 0.265 Hom.: 3085

Bravo AF: 0.247

Asia WGS AF: 0.394 AC: 1369 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.3
DANN	Benign	0.46
PhyloP100		0.68

Splicing

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

Other links and lift over

dbSNP: rs11238181; hg19: chr7-52225399;