2-203844626-C-G

Variant names:

• chr2-203844626-C-G
• rs231806

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 0.6 in 151,898 control chromosomes in the GnomAD database, including 27,642 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 0.60 (27642 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.127
• Publications: 16 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.733 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: 0.600 AC: 91028 AN: 151780 Hom.: 27597 Cov.: 31

Gnomad AFR AF: 0.628

Gnomad AMI AF: 0.582

Gnomad AMR AF: 0.579

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.403

Gnomad FIN AF: 0.692

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.583

Gnomad OTH AF: 0.553

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

GnomAD4 genome AF: 0.600 AC: 91130 AN: 151898 Hom.: 27642 Cov.: 31 AF XY: 0.603 AC XY: 44757 AN XY: 74248

African (AFR) AF: 0.628 AC: 26011 AN: 41418

American (AMR) AF: 0.579 AC: 8839 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.487 AC: 1684 AN: 3456

East Asian (EAS) AF: 0.753 AC: 3883 AN: 5160

South Asian (SAS) AF: 0.405 AC: 1947 AN: 4808

European-Finnish (FIN) AF: 0.692 AC: 7291 AN: 10542

Middle Eastern (MID) AF: 0.476 AC: 139 AN: 292

European-Non Finnish (NFE) AF: 0.583 AC: 39648 AN: 67950

Other (OTH) AF: 0.551 AC: 1158 AN: 2100

Alfa AF: 0.477 Hom.: 1355

Bravo AF: 0.597

Asia WGS AF: 0.546 AC: 1900 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.37
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs231806; hg19: chr2-204709349;