2-88859459-G-A

Position:

• chr2-88859459-G-A

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 0.151 in 148,736 control chromosomes in the GnomAD database, including 2,032 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 0.15 (2032 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.615

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.292 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22523 AN: 148676 Hom.: 2029 Cov.: 33

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.306

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.169

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.151 AC: 22532 AN: 148736 Hom.: 2032 Cov.: 33 AF XY: 0.152 AC XY: 11040 AN XY: 72442

Gnomad4 AFR AF: 0.109

Gnomad4 AMR AF: 0.246

Gnomad4 ASJ AF: 0.174

Gnomad4 EAS AF: 0.306

Gnomad4 SAS AF: 0.103

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.154

Gnomad4 OTH AF: 0.168

Alfa AF: 0.136 Hom.: 201

Bravo AF: 0.168

Asia WGS AF: 0.165 AC: 561 AN: 3416

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.4
DANN	Benign	0.35

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs232228; hg19: chr2-89158971;