2-189018918-A-G

Variant names:

• chr2-189018918-A-G
• rs7424137

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 0.59 in 152,142 control chromosomes in the GnomAD database, including 31,994 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 0.59 (31994 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.15
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.776 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.591 AC: 89798 AN: 152024 Hom.: 31986 Cov.: 33

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.643

Gnomad AMR AF: 0.640

Gnomad ASJ AF: 0.714

Gnomad EAS AF: 0.728

Gnomad SAS AF: 0.662

Gnomad FIN AF: 0.805

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.781

Gnomad OTH AF: 0.614

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

GnomAD4 genome AF: 0.590 AC: 89813 AN: 152142 Hom.: 31994 Cov.: 33 AF XY: 0.595 AC XY: 44234 AN XY: 74382

African (AFR) AF: 0.166 AC: 6895 AN: 41518

American (AMR) AF: 0.641 AC: 9797 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.714 AC: 2478 AN: 3470

East Asian (EAS) AF: 0.727 AC: 3759 AN: 5170

South Asian (SAS) AF: 0.664 AC: 3200 AN: 4820

European-Finnish (FIN) AF: 0.805 AC: 8520 AN: 10588

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.781 AC: 53100 AN: 67976

Other (OTH) AF: 0.615 AC: 1298 AN: 2112

Alfa AF: 0.708 Hom.: 121995

Bravo AF: 0.557

Asia WGS AF: 0.635 AC: 2208 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.6
DANN	Benign	0.74
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs7424137; hg19: chr2-189883644;