2-193610546-C-G

Variant names:

• chr2-193610546-C-G
• rs1020941

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 0.289 in 151,628 control chromosomes in the GnomAD database, including 6,864 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 0.29 (6864 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.763
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.419 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: 0.289 AC: 43804 AN: 151520 Hom.: 6858 Cov.: 31

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.419

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.289 AC: 43836 AN: 151628 Hom.: 6864 Cov.: 31 AF XY: 0.294 AC XY: 21793 AN XY: 74120

African (AFR) AF: 0.193 AC: 7993 AN: 41406

American (AMR) AF: 0.428 AC: 6521 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.208 AC: 722 AN: 3470

East Asian (EAS) AF: 0.419 AC: 2165 AN: 5168

South Asian (SAS) AF: 0.429 AC: 2064 AN: 4806

European-Finnish (FIN) AF: 0.249 AC: 2582 AN: 10380

Middle Eastern (MID) AF: 0.295 AC: 86 AN: 292

European-Non Finnish (NFE) AF: 0.307 AC: 20844 AN: 67854

Other (OTH) AF: 0.302 AC: 635 AN: 2106

Alfa AF: 0.299 Hom.: 903

Bravo AF: 0.296

Asia WGS AF: 0.396 AC: 1370 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.55
DANN	Benign	0.34
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs1020941; hg19: chr2-194475270;