10-62850180-C-T

Position:

• chr10-62850180-C-T

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 0.479 in 152,062 control chromosomes in the GnomAD database, including 17,598 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 0.48 (17598 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.178

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.62850180C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000289487	ENST00000493899.2	n.542-34211G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.479 AC: 72781 AN: 151944 Hom.: 17585 Cov.: 32

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.518

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.391

Gnomad SAS AF: 0.492

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.476

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

GnomAD4 genome AF: 0.479 AC: 72842 AN: 152062 Hom.: 17598 Cov.: 32 AF XY: 0.483 AC XY: 35903 AN XY: 74332

Gnomad4 AFR AF: 0.433

Gnomad4 AMR AF: 0.420

Gnomad4 ASJ AF: 0.473

Gnomad4 EAS AF: 0.392

Gnomad4 SAS AF: 0.492

Gnomad4 FIN AF: 0.533

Gnomad4 NFE AF: 0.518

Gnomad4 OTH AF: 0.476

Alfa AF: 0.504 Hom.: 3297

Bravo AF: 0.465

Asia WGS AF: 0.470 AC: 1630 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.2
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1412554; hg19: chr10-64609940;