10-53034019-T-G

Position:

• chr10-53034019-T-G

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 0.774 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.235

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.53034019T>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.844

Gnomad4 AMR AF: 0.745

Gnomad4 ASJ AF: 0.794

Gnomad4 EAS AF: 0.708

Gnomad4 SAS AF: 0.794

Gnomad4 FIN AF: 0.793

Gnomad4 NFE AF: 0.737

Gnomad4 OTH AF: 0.769

Alfa AF: 0.766 Hom.: 6348

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2462479; hg19: chr10-54793779;