2-203836831-A-G

Variant names:

• chr2-203836831-A-G
• rs12992492

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 0.403 in 151,964 control chromosomes in the GnomAD database, including 12,733 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 0.40 (12733 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.697
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.64 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: 0.403 AC: 61142 AN: 151846 Hom.: 12718 Cov.: 31

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.659

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.520

Gnomad MID AF: 0.258

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.403 AC: 61204 AN: 151964 Hom.: 12733 Cov.: 31 AF XY: 0.409 AC XY: 30429 AN XY: 74310

African (AFR) AF: 0.377 AC: 15607 AN: 41436

American (AMR) AF: 0.413 AC: 6313 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.301 AC: 1043 AN: 3464

East Asian (EAS) AF: 0.659 AC: 3399 AN: 5160

South Asian (SAS) AF: 0.331 AC: 1593 AN: 4806

European-Finnish (FIN) AF: 0.520 AC: 5493 AN: 10558

Middle Eastern (MID) AF: 0.274 AC: 80 AN: 292

European-Non Finnish (NFE) AF: 0.390 AC: 26524 AN: 67954

Other (OTH) AF: 0.361 AC: 761 AN: 2110

Alfa AF: 0.402 Hom.: 1740

Bravo AF: 0.398

Asia WGS AF: 0.453 AC: 1572 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.2
DANN	Benign	0.35
PhyloP100		0.70

Splicing

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

Other links and lift over

dbSNP: rs12992492; hg19: chr2-204701554;