2-196610770-C-T

Variant names:

• chr2-196610770-C-T
• rs12989157

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 0.806 in 152,004 control chromosomes in the GnomAD database, including 49,839 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 0.81 (49839 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.942 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.806 AC: 122452 AN: 151886 Hom.: 49811 Cov.: 31

Gnomad AFR AF: 0.691

Gnomad AMI AF: 0.648

Gnomad AMR AF: 0.863

Gnomad ASJ AF: 0.843

Gnomad EAS AF: 0.965

Gnomad SAS AF: 0.873

Gnomad FIN AF: 0.878

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.837

Gnomad OTH AF: 0.796

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

GnomAD4 genome AF: 0.806 AC: 122524 AN: 152004 Hom.: 49839 Cov.: 31 AF XY: 0.810 AC XY: 60132 AN XY: 74264

African (AFR) AF: 0.690 AC: 28604 AN: 41434

American (AMR) AF: 0.863 AC: 13194 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.843 AC: 2926 AN: 3472

East Asian (EAS) AF: 0.965 AC: 4921 AN: 5100

South Asian (SAS) AF: 0.874 AC: 4203 AN: 4810

European-Finnish (FIN) AF: 0.878 AC: 9299 AN: 10594

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.837 AC: 56876 AN: 67986

Other (OTH) AF: 0.798 AC: 1687 AN: 2114

Alfa AF: 0.825 Hom.: 6486

Bravo AF: 0.799

Asia WGS AF: 0.903 AC: 3143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.1
DANN	Benign	0.68
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs12989157; hg19: chr2-197475494;