7-52452881-C-T

Variant names:

• chr7-52452881-C-T
• rs10266118

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 0.646 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.646 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

Gnomad4 AFR AF: 0.590

Gnomad4 AMR AF: 0.608

Gnomad4 ASJ AF: 0.722

Gnomad4 EAS AF: 0.875

Gnomad4 SAS AF: 0.712

Gnomad4 FIN AF: 0.657

Gnomad4 NFE AF: 0.659

Gnomad4 OTH AF: 0.668

Alfa AF: 0.573 Hom.: 2973

Bravo AF: 0.638

Asia WGS AF: 0.754 AC: 2621 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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