chr10-52759208-C-T

Position:

• chr10-52759208-C-T

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 0.655 in 151,938 control chromosomes in the GnomAD database, including 34,789 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 (34789 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.202

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.776 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.655 AC: 99479 AN: 151820 Hom.: 34781 Cov.: 31

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.718

Gnomad AMR AF: 0.725

Gnomad ASJ AF: 0.793

Gnomad EAS AF: 0.745

Gnomad SAS AF: 0.797

Gnomad FIN AF: 0.750

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.760

Gnomad OTH AF: 0.669

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

GnomAD4 genome AF: 0.655 AC: 99508 AN: 151938 Hom.: 34789 Cov.: 31 AF XY: 0.659 AC XY: 48894 AN XY: 74232

Gnomad4 AFR AF: 0.390

Gnomad4 AMR AF: 0.726

Gnomad4 ASJ AF: 0.793

Gnomad4 EAS AF: 0.746

Gnomad4 SAS AF: 0.797

Gnomad4 FIN AF: 0.750

Gnomad4 NFE AF: 0.760

Gnomad4 OTH AF: 0.671

Alfa AF: 0.744 Hom.: 57493

Bravo AF: 0.640

Asia WGS AF: 0.761 AC: 2644 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.3
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs920727; hg19: chr10-54518968;