rs12619554

Variant names:

• chr2-17171105-G-A
• rs12619554
• ENST00000845015.1:n.253+22259C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000845015.1(ENSG00000309887):​n.253+22259C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000309887 ENST00000845015.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.522
• Publications: 2 publications found

Genes affected

ENSG00000309887 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000309887	ENST00000845015.1	n.253+22259C>T		intron_variant	Intron 1 of 2
ENSG00000309887	ENST00000845016.1	n.106+441C>T		intron_variant	Intron 1 of 2

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

African (AFR) AF: 0.0942 AC: 3909 AN: 41506

American (AMR) AF: 0.208 AC: 3178 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0207 AC: 72 AN: 3472

East Asian (EAS) AF: 0.766 AC: 3947 AN: 5154

South Asian (SAS) AF: 0.215 AC: 1036 AN: 4814

European-Finnish (FIN) AF: 0.185 AC: 1960 AN: 10574

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0479 AC: 3256 AN: 67990

Other (OTH) AF: 0.136 AC: 287 AN: 2116

Alfa AF: 0.0671 Hom.: 1189

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
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs12619554; hg19: chr2-17352372;