chr2-16924585-C-T

Variant names:

• chr2-16924585-C-T
• rs2042079

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 0.369 in 151,632 control chromosomes in the GnomAD database, including 12,133 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 0.37 (12133 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 4 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 = 0.724 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: 0.368 AC: 55822 AN: 151514 Hom.: 12099 Cov.: 32

Gnomad AFR AF: 0.543

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.743

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.336

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

GnomAD4 genome AF: 0.369 AC: 55925 AN: 151632 Hom.: 12133 Cov.: 32 AF XY: 0.372 AC XY: 27595 AN XY: 74094

African (AFR) AF: 0.543 AC: 22472 AN: 41376

American (AMR) AF: 0.394 AC: 5991 AN: 15190

Ashkenazi Jewish (ASJ) AF: 0.353 AC: 1222 AN: 3460

East Asian (EAS) AF: 0.744 AC: 3849 AN: 5176

South Asian (SAS) AF: 0.334 AC: 1607 AN: 4812

European-Finnish (FIN) AF: 0.294 AC: 3095 AN: 10534

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.245 AC: 16604 AN: 67776

Other (OTH) AF: 0.340 AC: 715 AN: 2102

Alfa AF: 0.289 Hom.: 5586

Bravo AF: 0.393

Asia WGS AF: 0.542 AC: 1874 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.19
DANN	Benign	0.34
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2042079; hg19: chr2-17105852;