chr2-189018918-A-G

Position:

• chr2-189018918-A-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.166

Gnomad4 AMR AF: 0.641

Gnomad4 ASJ AF: 0.714

Gnomad4 EAS AF: 0.727

Gnomad4 SAS AF: 0.664

Gnomad4 FIN AF: 0.805

Gnomad4 NFE AF: 0.781

Gnomad4 OTH AF: 0.615

Alfa AF: 0.738 Hom.: 80476

Bravo AF: 0.557

Asia WGS AF: 0.635 AC: 2208 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7424137; hg19: chr2-189883644;