2-27495607-T-C

Variant names:

• chr2-27495607-T-C
• rs780090

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 0.942 in 152,326 control chromosomes in the GnomAD database, including 67,679 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 0.94 (67679 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.535
• Publications: 22 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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: 0.942 AC: 143391 AN: 152208 Hom.: 67614 Cov.: 32

Gnomad AFR AF: 0.975

Gnomad AMI AF: 0.918

Gnomad AMR AF: 0.947

Gnomad ASJ AF: 0.941

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.986

Gnomad FIN AF: 0.944

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.914

Gnomad OTH AF: 0.928

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

GnomAD4 genome AF: 0.942 AC: 143516 AN: 152326 Hom.: 67679 Cov.: 32 AF XY: 0.944 AC XY: 70302 AN XY: 74478

African (AFR) AF: 0.975 AC: 40550 AN: 41588

American (AMR) AF: 0.947 AC: 14495 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.941 AC: 3267 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5176 AN: 5178

South Asian (SAS) AF: 0.986 AC: 4759 AN: 4826

European-Finnish (FIN) AF: 0.944 AC: 10017 AN: 10612

Middle Eastern (MID) AF: 0.922 AC: 271 AN: 294

European-Non Finnish (NFE) AF: 0.914 AC: 62182 AN: 68026

Other (OTH) AF: 0.929 AC: 1962 AN: 2112

Alfa AF: 0.923 Hom.: 107780

Bravo AF: 0.943

Asia WGS AF: 0.989 AC: 3438 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	12
DANN	Benign	0.81
PhyloP100		-0.54
PromoterAI		0.0029	Neutral

Splicing

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

Other links and lift over

dbSNP: rs780090; hg19: chr2-27718474;