2-226204806-T-C

Variant names:

• chr2-226204806-T-C
• rs2972150

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 0.458 in 151,214 control chromosomes in the GnomAD database, including 16,420 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 0.46 (16420 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.204
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.529 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: 0.458 AC: 69157 AN: 151096 Hom.: 16403 Cov.: 31

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.401

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.485

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

GnomAD4 genome AF: 0.458 AC: 69188 AN: 151214 Hom.: 16420 Cov.: 31 AF XY: 0.453 AC XY: 33436 AN XY: 73868

African (AFR) AF: 0.325 AC: 13451 AN: 41360

American (AMR) AF: 0.471 AC: 7144 AN: 15154

Ashkenazi Jewish (ASJ) AF: 0.617 AC: 2127 AN: 3450

East Asian (EAS) AF: 0.462 AC: 2367 AN: 5126

South Asian (SAS) AF: 0.547 AC: 2631 AN: 4812

European-Finnish (FIN) AF: 0.409 AC: 4299 AN: 10512

Middle Eastern (MID) AF: 0.397 AC: 116 AN: 292

European-Non Finnish (NFE) AF: 0.526 AC: 35534 AN: 67492

Other (OTH) AF: 0.491 AC: 1035 AN: 2106

Alfa AF: 0.338 Hom.: 879

Bravo AF: 0.453

Asia WGS AF: 0.574 AC: 1997 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.83
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs2972150; hg19: chr2-227069522;