2-226235138-T-C

Variant names:

• chr2-226235138-T-C
• rs2972147

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 0.672 in 152,052 control chromosomes in the GnomAD database, including 34,509 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 0.67 (34509 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72
• Publications: 23 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.905 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.672 AC: 102025 AN: 151934 Hom.: 34474 Cov.: 31

Gnomad AFR AF: 0.672

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.736

Gnomad ASJ AF: 0.712

Gnomad EAS AF: 0.926

Gnomad SAS AF: 0.769

Gnomad FIN AF: 0.626

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.638

Gnomad OTH AF: 0.662

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

GnomAD4 genome AF: 0.672 AC: 102110 AN: 152052 Hom.: 34509 Cov.: 31 AF XY: 0.673 AC XY: 50032 AN XY: 74314

African (AFR) AF: 0.671 AC: 27831 AN: 41462

American (AMR) AF: 0.737 AC: 11261 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.712 AC: 2468 AN: 3468

East Asian (EAS) AF: 0.927 AC: 4791 AN: 5170

South Asian (SAS) AF: 0.769 AC: 3712 AN: 4824

European-Finnish (FIN) AF: 0.626 AC: 6612 AN: 10556

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.638 AC: 43359 AN: 67974

Other (OTH) AF: 0.666 AC: 1403 AN: 2108

Alfa AF: 0.656 Hom.: 49429

Bravo AF: 0.681

Asia WGS AF: 0.847 AC: 2944 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.23
DANN	Benign	0.48
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs2972147; hg19: chr2-227099854;