2-166692853-T-G

Variant names:

• chr2-166692853-T-G
• rs12619000

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 0.615 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.343

Gnomad4 AMR AF: 0.722

Gnomad4 ASJ AF: 0.639

Gnomad4 EAS AF: 0.568

Gnomad4 SAS AF: 0.535

Gnomad4 FIN AF: 0.723

Gnomad4 NFE AF: 0.747

Gnomad4 OTH AF: 0.632

Alfa AF: 0.721 Hom.: 57737

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12619000; hg19: chr2-167549363;