7-23715296-G-A

Variant names:

• chr7-23715296-G-A
• rs1559012
• NM_031414.5:c.151-2185G>A

Variant summary

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

The NM_031414.5(STK31):​c.151-2185G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 151,830 control chromosomes in the GnomAD database, including 5,410 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 0.26 (5410 hom., cov: 30)
• Consequence: STK31 NM_031414.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.981
• Publications: 5 publications found

Genes affected

STK31 (HGNC:11407): (serine/threonine kinase 31) This gene is similar to a mouse gene that encodes a putative protein kinase with a tudor domain, and shows testis-specific expression. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.381 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_031414.5. 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
	STK31	NM_031414.5	MANE Select	c.151-2185G>A		intron	N/A	NP_113602.2
	STK31	NM_001260504.2		c.82-2185G>A		intron	N/A	NP_001247433.1
	STK31	NM_001260505.2		c.151-2185G>A		intron	N/A	NP_001247434.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STK31	ENST00000355870.8	TSL:1 MANE Select	c.151-2185G>A		intron	N/A	ENSP00000348132.3
	STK31	ENST00000354639.7	TSL:1	c.82-2185G>A		intron	N/A	ENSP00000346660.3
	STK31	ENST00000433467.6	TSL:2	c.151-2185G>A		intron	N/A	ENSP00000411852.2

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38891 AN: 151712 Hom.: 5416 Cov.: 30

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.397

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.256 AC: 38879 AN: 151830 Hom.: 5410 Cov.: 30 AF XY: 0.259 AC XY: 19242 AN XY: 74226

African (AFR) AF: 0.157 AC: 6490 AN: 41408

American (AMR) AF: 0.221 AC: 3376 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.285 AC: 989 AN: 3466

East Asian (EAS) AF: 0.396 AC: 2040 AN: 5156

South Asian (SAS) AF: 0.345 AC: 1661 AN: 4808

European-Finnish (FIN) AF: 0.336 AC: 3537 AN: 10512

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.292 AC: 19811 AN: 67916

Other (OTH) AF: 0.268 AC: 563 AN: 2100

Alfa AF: 0.277 Hom.: 3450

Bravo AF: 0.241

Asia WGS AF: 0.318 AC: 1102 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.95
DANN	Benign	0.68
PhyloP100		-0.98
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1559012; hg19: chr7-23754915;