rs12619554

Variant names:

• chr2-17171105-G-A
• rs12619554

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 0.116 in 152,108 control chromosomes in the GnomAD database, including 2,547 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 (2547 hom., cov: 32)
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.746 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: 0.116 AC: 17640 AN: 151990 Hom.: 2540 Cov.: 32

Gnomad AFR AF: 0.0944

Gnomad AMI AF: 0.0165

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.0207

Gnomad EAS AF: 0.766

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0479

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.116 AC: 17669 AN: 152108 Hom.: 2547 Cov.: 32 AF XY: 0.129 AC XY: 9578 AN XY: 74352

Gnomad4 AFR AF: 0.0942

Gnomad4 AMR AF: 0.208

Gnomad4 ASJ AF: 0.0207

Gnomad4 EAS AF: 0.766

Gnomad4 SAS AF: 0.215

Gnomad4 FIN AF: 0.185

Gnomad4 NFE AF: 0.0479

Gnomad4 OTH AF: 0.136

Alfa AF: 0.0639 Hom.: 881

Bravo AF: 0.119

Asia WGS AF: 0.488 AC: 1697 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.1
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12619554; hg19: chr2-17352372;