2-238943130-G-A

Variant names:

• chr2-238943130-G-A
• rs4521068

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 0.164 in 152,170 control chromosomes in the GnomAD database, including 2,587 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 0.16 (2587 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.350
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.32 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: 0.164 AC: 24938 AN: 152054 Hom.: 2589 Cov.: 32

Gnomad AFR AF: 0.0498

Gnomad AMI AF: 0.172

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.164 AC: 24926 AN: 152170 Hom.: 2587 Cov.: 32 AF XY: 0.165 AC XY: 12258 AN XY: 74396

African (AFR) AF: 0.0496 AC: 2061 AN: 41524

American (AMR) AF: 0.139 AC: 2130 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.222 AC: 769 AN: 3470

East Asian (EAS) AF: 0.333 AC: 1724 AN: 5170

South Asian (SAS) AF: 0.153 AC: 739 AN: 4820

European-Finnish (FIN) AF: 0.216 AC: 2284 AN: 10582

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.215 AC: 14624 AN: 67984

Other (OTH) AF: 0.178 AC: 376 AN: 2110

Alfa AF: 0.194 Hom.: 9935

Bravo AF: 0.155

Asia WGS AF: 0.208 AC: 726 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.98
DANN	Benign	0.71
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs4521068; hg19: chr2-239864826;