2-17863421-C-T

Variant names:

• chr2-17863421-C-T
• rs12996816

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 0.0935 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0231 AC: 960 AN: 41528

American (AMR) AF: 0.102 AC: 1567 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.204 AC: 706 AN: 3466

East Asian (EAS) AF: 0.0772 AC: 400 AN: 5178

South Asian (SAS) AF: 0.0906 AC: 437 AN: 4824

European-Finnish (FIN) AF: 0.0999 AC: 1058 AN: 10590

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.128 AC: 8712 AN: 68002

Other (OTH) AF: 0.117 AC: 246 AN: 2108

Alfa AF: 0.119 Hom.: 708

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
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs12996816; hg19: chr2-18044688;