10-61602229-C-T

Position:

• chr10-61602229-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 0.778 in 151,766 control chromosomes in the GnomAD database, including 46,296 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 0.78 (46296 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.832 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.61602229C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.777 AC: 117889 AN: 151648 Hom.: 46224 Cov.: 31

Gnomad AFR AF: 0.839

Gnomad AMI AF: 0.833

Gnomad AMR AF: 0.789

Gnomad ASJ AF: 0.804

Gnomad EAS AF: 0.550

Gnomad SAS AF: 0.583

Gnomad FIN AF: 0.831

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.758

Gnomad OTH AF: 0.773

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

GnomAD4 genome AF: 0.778 AC: 118024 AN: 151766 Hom.: 46296 Cov.: 31 AF XY: 0.777 AC XY: 57612 AN XY: 74164

Gnomad4 AFR AF: 0.839

Gnomad4 AMR AF: 0.789

Gnomad4 ASJ AF: 0.804

Gnomad4 EAS AF: 0.550

Gnomad4 SAS AF: 0.585

Gnomad4 FIN AF: 0.831

Gnomad4 NFE AF: 0.758

Gnomad4 OTH AF: 0.775

Alfa AF: 0.762 Hom.: 91061

Bravo AF: 0.782

Asia WGS AF: 0.601 AC: 2089 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.12
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2814021; hg19: chr10-63361987;