10-43188152-C-T

Variant names:

• chr10-43188152-C-T
• rs2435377

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 0.837 in 152,166 control chromosomes in the GnomAD database, including 53,921 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 0.84 (53921 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0300

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.929 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: 0.837 AC: 127251 AN: 152048 Hom.: 53864 Cov.: 31

Gnomad AFR AF: 0.937

Gnomad AMI AF: 0.920

Gnomad AMR AF: 0.807

Gnomad ASJ AF: 0.765

Gnomad EAS AF: 0.501

Gnomad SAS AF: 0.710

Gnomad FIN AF: 0.822

Gnomad MID AF: 0.790

Gnomad NFE AF: 0.823

Gnomad OTH AF: 0.821

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

GnomAD4 genome AF: 0.837 AC: 127373 AN: 152166 Hom.: 53921 Cov.: 31 AF XY: 0.834 AC XY: 62012 AN XY: 74366

Gnomad4 AFR AF: 0.937

Gnomad4 AMR AF: 0.807

Gnomad4 ASJ AF: 0.765

Gnomad4 EAS AF: 0.501

Gnomad4 SAS AF: 0.711

Gnomad4 FIN AF: 0.822

Gnomad4 NFE AF: 0.823

Gnomad4 OTH AF: 0.820

Alfa AF: 0.816 Hom.: 11024

Bravo AF: 0.843

Asia WGS AF: 0.623 AC: 2167 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.9
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2435377; hg19: chr10-43683600;