2-17863421-C-T

Variant names:

• chr2-17863421-C-T
• rs12996816

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 0.0935 in 152,194 control chromosomes in the GnomAD database, including 832 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 0.093 (832 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.522

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.126 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: 0.0936 AC: 14233 AN: 152076 Hom.: 835 Cov.: 33

Gnomad AFR AF: 0.0232

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.0775

Gnomad SAS AF: 0.0903

Gnomad FIN AF: 0.0999

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.0935 AC: 14228 AN: 152194 Hom.: 832 Cov.: 33 AF XY: 0.0921 AC XY: 6852 AN XY: 74414

Gnomad4 AFR AF: 0.0231

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.204

Gnomad4 EAS AF: 0.0772

Gnomad4 SAS AF: 0.0906

Gnomad4 FIN AF: 0.0999

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.117

Alfa AF: 0.119 Hom.: 645

Bravo AF: 0.0913

Asia WGS AF: 0.0570 AC: 198 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.2
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12996816; hg19: chr2-18044688;