2-237851475-A-G

Variant names:

• chr2-237851475-A-G
• rs1198823

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 0.362 in 152,116 control chromosomes in the GnomAD database, including 10,146 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 0.36 (10146 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.362
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.417 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: 0.362 AC: 55000 AN: 151998 Hom.: 10141 Cov.: 33

Gnomad AFR AF: 0.393

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.362 AC: 55016 AN: 152116 Hom.: 10146 Cov.: 33 AF XY: 0.364 AC XY: 27071 AN XY: 74368

African (AFR) AF: 0.393 AC: 16311 AN: 41474

American (AMR) AF: 0.409 AC: 6252 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.380 AC: 1319 AN: 3468

East Asian (EAS) AF: 0.160 AC: 832 AN: 5184

South Asian (SAS) AF: 0.432 AC: 2082 AN: 4818

European-Finnish (FIN) AF: 0.352 AC: 3726 AN: 10584

Middle Eastern (MID) AF: 0.408 AC: 119 AN: 292

European-Non Finnish (NFE) AF: 0.342 AC: 23248 AN: 67980

Other (OTH) AF: 0.368 AC: 777 AN: 2114

Alfa AF: 0.351 Hom.: 17816

Bravo AF: 0.361

Asia WGS AF: 0.276 AC: 964 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.19
DANN	Benign	0.68
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs1198823; hg19: chr2-238760118;