rs12619554

Positions:

• chr2-17171105-G-A

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;