2-61594736-C-T

Variant names:

• chr2-61594736-C-T
• rs6545886

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.976 AC: 40480 AN: 41496

American (AMR) AF: 0.883 AC: 13468 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.948 AC: 3291 AN: 3472

East Asian (EAS) AF: 0.998 AC: 5175 AN: 5186

South Asian (SAS) AF: 0.954 AC: 4596 AN: 4818

European-Finnish (FIN) AF: 0.926 AC: 9787 AN: 10564

Middle Eastern (MID) AF: 0.949 AC: 279 AN: 294

European-Non Finnish (NFE) AF: 0.888 AC: 60395 AN: 67998

Other (OTH) AF: 0.935 AC: 1974 AN: 2112

Alfa AF: 0.898 Hom.: 65722

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
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs6545886; hg19: chr2-61821871;