2-116938842-C-T

Variant names:

• chr2-116938842-C-T
• rs7592730

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 0.426 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.553 AC: 22886 AN: 41396

American (AMR) AF: 0.411 AC: 6260 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.381 AC: 1320 AN: 3468

East Asian (EAS) AF: 0.319 AC: 1634 AN: 5124

South Asian (SAS) AF: 0.354 AC: 1701 AN: 4804

European-Finnish (FIN) AF: 0.427 AC: 4500 AN: 10528

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.367 AC: 24956 AN: 67960

Other (OTH) AF: 0.400 AC: 840 AN: 2100

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
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs7592730; hg19: chr2-117696418;