rs558912

Variant names:

• chr2-16809986-T-C
• rs558912

Your query was ambiguous. Multiple possible variants found:

• chr2-16809986-T-C
• chr2-16809986-T-G

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 0.591 in 152,032 control chromosomes in the GnomAD database, including 26,893 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 0.59 (26893 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.631 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: 0.591 AC: 89820 AN: 151914 Hom.: 26892 Cov.: 32

Gnomad AFR AF: 0.638

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.605

Gnomad OTH AF: 0.570

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

GnomAD4 genome AF: 0.591 AC: 89865 AN: 152032 Hom.: 26893 Cov.: 32 AF XY: 0.584 AC XY: 43346 AN XY: 74278

Gnomad4 AFR AF: 0.638

Gnomad4 AMR AF: 0.534

Gnomad4 ASJ AF: 0.627

Gnomad4 EAS AF: 0.347

Gnomad4 SAS AF: 0.469

Gnomad4 FIN AF: 0.575

Gnomad4 NFE AF: 0.605

Gnomad4 OTH AF: 0.572

Alfa AF: 0.589 Hom.: 42327

Bravo AF: 0.588

Asia WGS AF: 0.436 AC: 1519 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.1
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs558912; hg19: chr2-16991253;