5-147178371-T-C

Variant names:

• chr5-147178371-T-C
• rs1897527
• ENST00000761977.1:n.985-882A>G

Variant summary

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

The ENST00000761977.1(STK32A-AS1):​n.985-882A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.715 in 152,076 control chromosomes in the GnomAD database, including 39,369 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 0.72 (39369 hom., cov: 33)
• Consequence: STK32A-AS1 ENST00000761977.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 1 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.803 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000761977.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STK32A-AS1	NR_147190.1		n.1157-882A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STK32A-AS1	ENST00000761977.1		n.985-882A>G		intron	N/A
	STK32A-AS1	ENST00000761978.1		n.350-882A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.715 AC: 108662 AN: 151958 Hom.: 39314 Cov.: 33

Gnomad AFR AF: 0.811

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.789

Gnomad ASJ AF: 0.724

Gnomad EAS AF: 0.729

Gnomad SAS AF: 0.789

Gnomad FIN AF: 0.629

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.646

Gnomad OTH AF: 0.755

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

GnomAD4 genome AF: 0.715 AC: 108774 AN: 152076 Hom.: 39369 Cov.: 33 AF XY: 0.716 AC XY: 53253 AN XY: 74324

African (AFR) AF: 0.811 AC: 33672 AN: 41536

American (AMR) AF: 0.789 AC: 12042 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.724 AC: 2515 AN: 3472

East Asian (EAS) AF: 0.730 AC: 3775 AN: 5174

South Asian (SAS) AF: 0.788 AC: 3798 AN: 4818

European-Finnish (FIN) AF: 0.629 AC: 6636 AN: 10548

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.646 AC: 43901 AN: 67952

Other (OTH) AF: 0.757 AC: 1595 AN: 2108

Alfa AF: 0.675 Hom.: 4375

Bravo AF: 0.733

Asia WGS AF: 0.796 AC: 2769 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.17
DANN	Benign	0.72
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1897527; hg19: chr5-146557934;