2-166692853-T-G

Variant names:

• chr2-166692853-T-G
• rs12619000

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 0.615 in 151,810 control chromosomes in the GnomAD database, including 31,206 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 0.62 (31206 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.741 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: 0.616 AC: 93407 AN: 151692 Hom.: 31201 Cov.: 30

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.719

Gnomad AMR AF: 0.722

Gnomad ASJ AF: 0.639

Gnomad EAS AF: 0.568

Gnomad SAS AF: 0.535

Gnomad FIN AF: 0.723

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.747

Gnomad OTH AF: 0.636

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

GnomAD4 genome AF: 0.615 AC: 93428 AN: 151810 Hom.: 31206 Cov.: 30 AF XY: 0.615 AC XY: 45616 AN XY: 74192

African (AFR) AF: 0.343 AC: 14188 AN: 41384

American (AMR) AF: 0.722 AC: 11013 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.639 AC: 2220 AN: 3472

East Asian (EAS) AF: 0.568 AC: 2907 AN: 5122

South Asian (SAS) AF: 0.535 AC: 2565 AN: 4794

European-Finnish (FIN) AF: 0.723 AC: 7624 AN: 10548

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.747 AC: 50735 AN: 67930

Other (OTH) AF: 0.632 AC: 1332 AN: 2108

Alfa AF: 0.710 Hom.: 79494

Bravo AF: 0.608

Asia WGS AF: 0.545 AC: 1894 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.27
DANN	Benign	0.38
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs12619000; hg19: chr2-167549363;