10-53600475-C-T

Variant names:

• chr10-53600475-C-T
• rs2050381

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 0.677 in 152,120 control chromosomes in the GnomAD database, including 35,849 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 0.68 (35849 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.968 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: 0.677 AC: 102966 AN: 152002 Hom.: 35818 Cov.: 33

Gnomad AFR AF: 0.792

Gnomad AMI AF: 0.640

Gnomad AMR AF: 0.664

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.991

Gnomad SAS AF: 0.807

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.600

Gnomad OTH AF: 0.681

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

GnomAD4 genome AF: 0.677 AC: 103048 AN: 152120 Hom.: 35849 Cov.: 33 AF XY: 0.680 AC XY: 50604 AN XY: 74374

African (AFR) AF: 0.792 AC: 32882 AN: 41508

American (AMR) AF: 0.664 AC: 10142 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.563 AC: 1953 AN: 3468

East Asian (EAS) AF: 0.991 AC: 5127 AN: 5176

South Asian (SAS) AF: 0.806 AC: 3892 AN: 4828

European-Finnish (FIN) AF: 0.569 AC: 6013 AN: 10562

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.600 AC: 40800 AN: 67980

Other (OTH) AF: 0.685 AC: 1448 AN: 2114

Alfa AF: 0.528 Hom.: 1591

Bravo AF: 0.686

Asia WGS AF: 0.878 AC: 3050 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	0.45
DANN	Benign	0.40
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs2050381; hg19: chr10-55360235;