7-52452881-C-T

Variant names:

• chr7-52452881-C-T
• rs10266118

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 0.646 in 151,626 control chromosomes in the GnomAD database, including 31,811 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 0.65 (31811 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.854 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.646 AC: 97928 AN: 151508 Hom.: 31805 Cov.: 29

Gnomad AFR AF: 0.591

Gnomad AMI AF: 0.747

Gnomad AMR AF: 0.609

Gnomad ASJ AF: 0.722

Gnomad EAS AF: 0.875

Gnomad SAS AF: 0.710

Gnomad FIN AF: 0.657

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.659

Gnomad OTH AF: 0.665

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

GnomAD4 genome AF: 0.646 AC: 97974 AN: 151626 Hom.: 31811 Cov.: 29 AF XY: 0.650 AC XY: 48123 AN XY: 74070

African (AFR) AF: 0.590 AC: 24381 AN: 41300

American (AMR) AF: 0.608 AC: 9252 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.722 AC: 2501 AN: 3466

East Asian (EAS) AF: 0.875 AC: 4502 AN: 5146

South Asian (SAS) AF: 0.712 AC: 3421 AN: 4808

European-Finnish (FIN) AF: 0.657 AC: 6905 AN: 10508

Middle Eastern (MID) AF: 0.776 AC: 225 AN: 290

European-Non Finnish (NFE) AF: 0.659 AC: 44700 AN: 67866

Other (OTH) AF: 0.668 AC: 1409 AN: 2108

Alfa AF: 0.573 Hom.: 3099

Bravo AF: 0.638

Asia WGS AF: 0.754 AC: 2621 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.49
DANN	Benign	0.14
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs10266118; hg19: chr7-52520577; COSMIC: COSV65418594;