rs12988998

Variant names:

• chr2-17287976-C-T
• rs12988998

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 0.206 in 151,796 control chromosomes in the GnomAD database, including 5,131 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 0.21 (5131 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.691
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.448 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: 0.206 AC: 31189 AN: 151678 Hom.: 5105 Cov.: 32

Gnomad AFR AF: 0.453

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.0382

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.0435

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.206 AC: 31267 AN: 151796 Hom.: 5131 Cov.: 32 AF XY: 0.199 AC XY: 14790 AN XY: 74160

African (AFR) AF: 0.453 AC: 18777 AN: 41406

American (AMR) AF: 0.128 AC: 1959 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 437 AN: 3466

East Asian (EAS) AF: 0.0379 AC: 196 AN: 5168

South Asian (SAS) AF: 0.125 AC: 601 AN: 4816

European-Finnish (FIN) AF: 0.0435 AC: 458 AN: 10536

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.123 AC: 8332 AN: 67842

Other (OTH) AF: 0.185 AC: 389 AN: 2102

Alfa AF: 0.136 Hom.: 1876

Bravo AF: 0.220

Asia WGS AF: 0.106 AC: 370 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.85
DANN	Benign	0.74
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs12988998; hg19: chr2-17469243;