2-116938842-C-T

Position:

• chr2-116938842-C-T

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 0.426 in 151,820 control chromosomes in the GnomAD database, including 14,236 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 0.43 (14236 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.03

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.547 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: 0.426 AC: 64589 AN: 151702 Hom.: 14206 Cov.: 32

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.411

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.319

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.426 AC: 64665 AN: 151820 Hom.: 14236 Cov.: 32 AF XY: 0.427 AC XY: 31645 AN XY: 74182

Gnomad4 AFR AF: 0.553

Gnomad4 AMR AF: 0.411

Gnomad4 ASJ AF: 0.381

Gnomad4 EAS AF: 0.319

Gnomad4 SAS AF: 0.354

Gnomad4 FIN AF: 0.427

Gnomad4 NFE AF: 0.367

Gnomad4 OTH AF: 0.400

Alfa AF: 0.220 Hom.: 441

Bravo AF: 0.432

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.71
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7592730; hg19: chr2-117696418;