rs12988908

Variant names:

• chr2-31851628-A-G
• rs12988908

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 0.115 in 152,044 control chromosomes in the GnomAD database, including 1,062 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 0.12 (1062 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0410

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.133 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: 0.115 AC: 17481 AN: 151926 Hom.: 1051 Cov.: 32

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.0804

Gnomad AMR AF: 0.0916

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.0883

Gnomad SAS AF: 0.0966

Gnomad FIN AF: 0.0984

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.115 AC: 17517 AN: 152044 Hom.: 1062 Cov.: 32 AF XY: 0.114 AC XY: 8486 AN XY: 74334

Gnomad4 AFR AF: 0.136

Gnomad4 AMR AF: 0.0915

Gnomad4 ASJ AF: 0.261

Gnomad4 EAS AF: 0.0881

Gnomad4 SAS AF: 0.0973

Gnomad4 FIN AF: 0.0984

Gnomad4 NFE AF: 0.106

Gnomad4 OTH AF: 0.123

Alfa AF: 0.111 Hom.: 129

Bravo AF: 0.117

Asia WGS AF: 0.101 AC: 352 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.0
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12988908; hg19: chr2-32076697;