2-108120219-C-T

Variant names:

• chr2-108120219-C-T
• rs931326

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 0.547 in 151,980 control chromosomes in the GnomAD database, including 23,599 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 0.55 (23599 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.236
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.876 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.547 AC: 83095 AN: 151862 Hom.: 23566 Cov.: 32

Gnomad AFR AF: 0.631

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.542

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.898

Gnomad SAS AF: 0.653

Gnomad FIN AF: 0.527

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.517

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

GnomAD4 genome AF: 0.547 AC: 83184 AN: 151980 Hom.: 23599 Cov.: 32 AF XY: 0.554 AC XY: 41113 AN XY: 74270

African (AFR) AF: 0.631 AC: 26171 AN: 41454

American (AMR) AF: 0.543 AC: 8292 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.493 AC: 1708 AN: 3468

East Asian (EAS) AF: 0.898 AC: 4635 AN: 5162

South Asian (SAS) AF: 0.652 AC: 3142 AN: 4816

European-Finnish (FIN) AF: 0.527 AC: 5560 AN: 10544

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.472 AC: 32099 AN: 67942

Other (OTH) AF: 0.522 AC: 1101 AN: 2110

Alfa AF: 0.493 Hom.: 23825

Bravo AF: 0.552

Asia WGS AF: 0.779 AC: 2706 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.20
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs931326; hg19: chr2-108736675;