10-43136250-C-T

Variant names:

• chr10-43136250-C-T
• rs3004214

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 0.795 in 151,966 control chromosomes in the GnomAD database, including 48,590 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 0.80 (48590 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.699
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.875 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: 0.795 AC: 120774 AN: 151848 Hom.: 48543 Cov.: 30

Gnomad AFR AF: 0.883

Gnomad AMI AF: 0.820

Gnomad AMR AF: 0.778

Gnomad ASJ AF: 0.732

Gnomad EAS AF: 0.501

Gnomad SAS AF: 0.640

Gnomad FIN AF: 0.809

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.781

Gnomad OTH AF: 0.776

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

GnomAD4 genome AF: 0.795 AC: 120882 AN: 151966 Hom.: 48590 Cov.: 30 AF XY: 0.793 AC XY: 58912 AN XY: 74256

African (AFR) AF: 0.883 AC: 36586 AN: 41446

American (AMR) AF: 0.778 AC: 11884 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.732 AC: 2541 AN: 3472

East Asian (EAS) AF: 0.501 AC: 2567 AN: 5124

South Asian (SAS) AF: 0.642 AC: 3084 AN: 4804

European-Finnish (FIN) AF: 0.809 AC: 8547 AN: 10566

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.781 AC: 53072 AN: 67978

Other (OTH) AF: 0.776 AC: 1630 AN: 2100

Alfa AF: 0.782 Hom.: 29751

Bravo AF: 0.801

Asia WGS AF: 0.600 AC: 2087 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.49
DANN	Benign	0.80
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs3004214; hg19: chr10-43631698;