rs12870589

Variant names:

• chr13-97572967-A-G
• rs12870589
• ENST00000802609.1:n.68-25616T>C

Variant summary

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

The ENST00000802609.1(ENSG00000304344):​n.68-25616T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.612 in 151,498 control chromosomes in the GnomAD database, including 30,648 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 0.61 (30648 hom., cov: 29)
• Consequence: ENSG00000304344 ENST00000802609.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.409
• Publications: 4 publications found

Genes affected

ENSG00000304344 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.722 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370324	XR_007063845.1	n.2615-25616T>C		intron_variant	Intron 3 of 5
LOC105370324	XR_931663.3	n.2671-25616T>C		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304344	ENST00000802609.1	n.68-25616T>C		intron_variant	Intron 1 of 2
ENSG00000304344	ENST00000802610.1	n.134+20661T>C		intron_variant	Intron 2 of 3
ENSG00000304344	ENST00000802611.1	n.138+20661T>C		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.613 AC: 92728 AN: 151382 Hom.: 30642 Cov.: 29

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.814

Gnomad AMR AF: 0.700

Gnomad ASJ AF: 0.759

Gnomad EAS AF: 0.476

Gnomad SAS AF: 0.704

Gnomad FIN AF: 0.719

Gnomad MID AF: 0.780

Gnomad NFE AF: 0.728

Gnomad OTH AF: 0.662

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

GnomAD4 genome AF: 0.612 AC: 92760 AN: 151498 Hom.: 30648 Cov.: 29 AF XY: 0.617 AC XY: 45626 AN XY: 74004

African (AFR) AF: 0.349 AC: 14424 AN: 41288

American (AMR) AF: 0.700 AC: 10645 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.759 AC: 2628 AN: 3462

East Asian (EAS) AF: 0.476 AC: 2444 AN: 5138

South Asian (SAS) AF: 0.705 AC: 3374 AN: 4788

European-Finnish (FIN) AF: 0.719 AC: 7525 AN: 10460

Middle Eastern (MID) AF: 0.767 AC: 224 AN: 292

European-Non Finnish (NFE) AF: 0.728 AC: 49370 AN: 67852

Other (OTH) AF: 0.662 AC: 1387 AN: 2096

Alfa AF: 0.695 Hom.: 128887

Bravo AF: 0.598

Asia WGS AF: 0.562 AC: 1956 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	14
DANN	Benign	0.87
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs12870589; hg19: chr13-98225221;