7-52157703-T-C

Variant names:

• chr7-52157703-T-C
• rs11238181

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 0.258 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.259 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

Gnomad4 AFR AF: 0.163

Gnomad4 AMR AF: 0.285

Gnomad4 ASJ AF: 0.345

Gnomad4 EAS AF: 0.449

Gnomad4 SAS AF: 0.417

Gnomad4 FIN AF: 0.359

Gnomad4 NFE AF: 0.265

Gnomad4 OTH AF: 0.259

Alfa AF: 0.265 Hom.: 2772

Bravo AF: 0.247

Asia WGS AF: 0.394 AC: 1369 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11238181; hg19: chr7-52225399;