chr2-108017094-G-T

Variant names:

• chr2-108017094-G-T
• rs333230

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 0.906 in 152,172 control chromosomes in the GnomAD database, including 62,741 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 0.91 (62741 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.710
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.971 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: 0.906 AC: 137740 AN: 152054 Hom.: 62678 Cov.: 31

Gnomad AFR AF: 0.976

Gnomad AMI AF: 0.846

Gnomad AMR AF: 0.914

Gnomad ASJ AF: 0.783

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.876

Gnomad FIN AF: 0.949

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.858

Gnomad OTH AF: 0.889

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

GnomAD4 genome AF: 0.906 AC: 137863 AN: 152172 Hom.: 62741 Cov.: 31 AF XY: 0.910 AC XY: 67717 AN XY: 74398

African (AFR) AF: 0.976 AC: 40563 AN: 41558

American (AMR) AF: 0.914 AC: 13954 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.783 AC: 2716 AN: 3468

East Asian (EAS) AF: 0.994 AC: 5131 AN: 5162

South Asian (SAS) AF: 0.877 AC: 4229 AN: 4822

European-Finnish (FIN) AF: 0.949 AC: 10043 AN: 10588

Middle Eastern (MID) AF: 0.799 AC: 235 AN: 294

European-Non Finnish (NFE) AF: 0.858 AC: 58342 AN: 67988

Other (OTH) AF: 0.889 AC: 1878 AN: 2112

Alfa AF: 0.883 Hom.: 11086

Bravo AF: 0.908

Asia WGS AF: 0.939 AC: 3262 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.35
DANN	Benign	0.39
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs333230; hg19: chr2-108633550;