2-108120219-C-T

Variant names:

• chr2-108120219-C-T
• rs931326

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 0.547 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.631

Gnomad4 AMR AF: 0.543

Gnomad4 ASJ AF: 0.493

Gnomad4 EAS AF: 0.898

Gnomad4 SAS AF: 0.652

Gnomad4 FIN AF: 0.527

Gnomad4 NFE AF: 0.472

Gnomad4 OTH AF: 0.522

Alfa AF: 0.486 Hom.: 17773

Bravo AF: 0.552

Asia WGS AF: 0.779 AC: 2706 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs931326; hg19: chr2-108736675;