2-61594736-C-T

Variant names:

• chr2-61594736-C-T
• rs6545886

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;