chr5-147177989-C-T

Variant names:

• chr5-147177989-C-T
• rs1432653
• ENST00000761977.1:n.985-500G>A

Variant summary

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

The ENST00000761977.1(STK32A-AS1):​n.985-500G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.652 in 151,924 control chromosomes in the GnomAD database, including 32,557 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 0.65 (32557 hom., cov: 32)
• Consequence: STK32A-AS1 ENST00000761977.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.815
• Publications: 3 publications found

Genes affected

STK32A-AS1 (HGNC:53468): (STK32A antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.767 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STK32A-AS1	NR_147190.1	n.1157-500G>A		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STK32A-AS1	ENST00000761977.1	n.985-500G>A		intron_variant	Intron 2 of 2
STK32A-AS1	ENST00000761978.1	n.350-500G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.652 AC: 98995 AN: 151806 Hom.: 32535 Cov.: 32

Gnomad AFR AF: 0.598

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.764

Gnomad ASJ AF: 0.724

Gnomad EAS AF: 0.727

Gnomad SAS AF: 0.788

Gnomad FIN AF: 0.631

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.642

Gnomad OTH AF: 0.702

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

GnomAD4 genome AF: 0.652 AC: 99063 AN: 151924 Hom.: 32557 Cov.: 32 AF XY: 0.655 AC XY: 48665 AN XY: 74266

African (AFR) AF: 0.598 AC: 24760 AN: 41430

American (AMR) AF: 0.765 AC: 11663 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.724 AC: 2513 AN: 3470

East Asian (EAS) AF: 0.728 AC: 3758 AN: 5160

South Asian (SAS) AF: 0.788 AC: 3795 AN: 4818

European-Finnish (FIN) AF: 0.631 AC: 6638 AN: 10524

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.642 AC: 43616 AN: 67958

Other (OTH) AF: 0.704 AC: 1487 AN: 2112

Alfa AF: 0.653 Hom.: 24096

Bravo AF: 0.662

Asia WGS AF: 0.779 AC: 2711 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	0.15
DANN	Benign	0.66
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs1432653; hg19: chr5-146557552;