2-170863118-T-C

Variant names:

• chr2-170863118-T-C
• rs12472230

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 0.915 in 152,118 control chromosomes in the GnomAD database, including 64,362 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 0.91 (64362 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.503
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.976 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: 0.915 AC: 139077 AN: 152000 Hom.: 64318 Cov.: 30

Gnomad AFR AF: 0.779

Gnomad AMI AF: 0.948

Gnomad AMR AF: 0.947

Gnomad ASJ AF: 0.974

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.970

Gnomad FIN AF: 0.995

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.982

Gnomad OTH AF: 0.927

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

GnomAD4 genome AF: 0.915 AC: 139177 AN: 152118 Hom.: 64362 Cov.: 30 AF XY: 0.916 AC XY: 68147 AN XY: 74374

African (AFR) AF: 0.780 AC: 32310 AN: 41442

American (AMR) AF: 0.947 AC: 14480 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.974 AC: 3381 AN: 3470

East Asian (EAS) AF: 0.757 AC: 3910 AN: 5166

South Asian (SAS) AF: 0.969 AC: 4670 AN: 4820

European-Finnish (FIN) AF: 0.995 AC: 10533 AN: 10590

Middle Eastern (MID) AF: 0.925 AC: 272 AN: 294

European-Non Finnish (NFE) AF: 0.982 AC: 66801 AN: 68024

Other (OTH) AF: 0.927 AC: 1957 AN: 2110

Alfa AF: 0.946 Hom.: 24872

Bravo AF: 0.904

Asia WGS AF: 0.895 AC: 3113 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.6
DANN	Benign	0.77
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs12472230; hg19: chr2-171719628;