2-231420200-T-C

Variant names:

• chr2-231420200-T-C
• rs4621162

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 0.379 in 151,324 control chromosomes in the GnomAD database, including 11,086 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 0.38 (11086 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.527
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.61 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: 0.379 AC: 57277 AN: 151212 Hom.: 11079 Cov.: 29

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.412

Gnomad EAS AF: 0.628

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.418

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.379 AC: 57312 AN: 151324 Hom.: 11086 Cov.: 29 AF XY: 0.380 AC XY: 28116 AN XY: 73960

African (AFR) AF: 0.330 AC: 13567 AN: 41120

American (AMR) AF: 0.344 AC: 5220 AN: 15186

Ashkenazi Jewish (ASJ) AF: 0.412 AC: 1425 AN: 3458

East Asian (EAS) AF: 0.628 AC: 3245 AN: 5164

South Asian (SAS) AF: 0.390 AC: 1874 AN: 4810

European-Finnish (FIN) AF: 0.418 AC: 4360 AN: 10432

Middle Eastern (MID) AF: 0.387 AC: 113 AN: 292

European-Non Finnish (NFE) AF: 0.388 AC: 26349 AN: 67848

Other (OTH) AF: 0.383 AC: 806 AN: 2106

Alfa AF: 0.389 Hom.: 6039

Bravo AF: 0.374

Asia WGS AF: 0.480 AC: 1673 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.4
DANN	Benign	0.78
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs4621162; hg19: chr2-232284911;