chr2-200276279-G-C

Variant names:

• chr2-200276279-G-C
• rs295136

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 0.431 in 151,920 control chromosomes in the GnomAD database, including 14,927 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 0.43 (14927 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.327
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.572 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65432 AN: 151802 Hom.: 14917 Cov.: 32

Gnomad AFR AF: 0.579

Gnomad AMI AF: 0.505

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.224

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.431 AC: 65463 AN: 151920 Hom.: 14927 Cov.: 32 AF XY: 0.425 AC XY: 31517 AN XY: 74228

African (AFR) AF: 0.578 AC: 23959 AN: 41422

American (AMR) AF: 0.322 AC: 4907 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.361 AC: 1253 AN: 3472

East Asian (EAS) AF: 0.224 AC: 1154 AN: 5158

South Asian (SAS) AF: 0.345 AC: 1660 AN: 4816

European-Finnish (FIN) AF: 0.361 AC: 3799 AN: 10536

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.402 AC: 27301 AN: 67956

Other (OTH) AF: 0.411 AC: 869 AN: 2112

Alfa AF: 0.408 Hom.: 1557

Bravo AF: 0.434

Asia WGS AF: 0.282 AC: 985 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.1
DANN	Benign	0.62
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs295136; hg19: chr2-201141002;