10-53034019-T-G

Variant names:

• chr10-53034019-T-G
• rs2462479

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 0.774 in 151,998 control chromosomes in the GnomAD database, including 45,597 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 0.77 (45597 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.235
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.837 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: 0.774 AC: 117487 AN: 151878 Hom.: 45568 Cov.: 33

Gnomad AFR AF: 0.844

Gnomad AMI AF: 0.757

Gnomad AMR AF: 0.745

Gnomad ASJ AF: 0.794

Gnomad EAS AF: 0.707

Gnomad SAS AF: 0.794

Gnomad FIN AF: 0.793

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.737

Gnomad OTH AF: 0.766

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

GnomAD4 genome AF: 0.774 AC: 117577 AN: 151998 Hom.: 45597 Cov.: 33 AF XY: 0.775 AC XY: 57572 AN XY: 74286

African (AFR) AF: 0.844 AC: 35038 AN: 41512

American (AMR) AF: 0.745 AC: 11373 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.794 AC: 2755 AN: 3468

East Asian (EAS) AF: 0.708 AC: 3653 AN: 5162

South Asian (SAS) AF: 0.794 AC: 3824 AN: 4816

European-Finnish (FIN) AF: 0.793 AC: 8376 AN: 10564

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.737 AC: 50037 AN: 67894

Other (OTH) AF: 0.769 AC: 1619 AN: 2106

Alfa AF: 0.755 Hom.: 13520

Bravo AF: 0.772

Asia WGS AF: 0.775 AC: 2683 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	8.9
DANN	Benign	0.79
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs2462479; hg19: chr10-54793779;