2-61594736-C-T

Position:

• chr2-61594736-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 0.922 in 152,098 control chromosomes in the GnomAD database, including 64,798 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 0.92 (64798 hom., cov: 30)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.61594736C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.922 AC: 140148 AN: 151980 Hom.: 64745 Cov.: 30

Gnomad AFR AF: 0.975

Gnomad AMI AF: 0.898

Gnomad AMR AF: 0.883

Gnomad ASJ AF: 0.948

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.954

Gnomad FIN AF: 0.926

Gnomad MID AF: 0.953

Gnomad NFE AF: 0.888

Gnomad OTH AF: 0.933

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

GnomAD4 genome AF: 0.922 AC: 140260 AN: 152098 Hom.: 64798 Cov.: 30 AF XY: 0.925 AC XY: 68766 AN XY: 74360

Gnomad4 AFR AF: 0.976

Gnomad4 AMR AF: 0.883

Gnomad4 ASJ AF: 0.948

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.954

Gnomad4 FIN AF: 0.926

Gnomad4 NFE AF: 0.888

Gnomad4 OTH AF: 0.935

Alfa AF: 0.898 Hom.: 42056

Bravo AF: 0.923

Asia WGS AF: 0.973 AC: 3384 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.25
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6545886; hg19: chr2-61821871;