rs1469000

Variant names:

• chr7-23770986-T-C
• rs1469000
• NM_031414.5:c.1714-19T>C

Your query was ambiguous. Multiple possible variants found:

• chr7-23770986-T-C
• chr7-23770986-T-G

Variant summary

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

The NM_031414.5(STK31):​c.1714-19T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.504 in 1,600,556 control chromosomes in the GnomAD database, including 205,611 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 0.46 (16814 hom., cov: 32)
  • Exomes 𝑓: 0.51 (188797 hom.)
• Consequence: STK31 NM_031414.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.621
• Publications: 12 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=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.539 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.1714-19T>C		intron	N/A	NP_113602.2
	STK31	NM_001260504.2		c.1645-19T>C		intron	N/A	NP_001247433.1
	STK31	NM_001260505.2		c.1714-19T>C		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.1714-19T>C		intron	N/A	ENSP00000348132.3
	STK31	ENST00000354639.7	TSL:1	c.1645-19T>C		intron	N/A	ENSP00000346660.3
	STK31	ENST00000405627.7	TSL:1	n.2239-19T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.464 AC: 70473 AN: 151868 Hom.: 16801 Cov.: 32

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.520

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.424

Gnomad EAS AF: 0.386

Gnomad SAS AF: 0.538

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.458

GnomAD2 exomes AF: 0.497 AC: 119519 AN: 240576 AF XY: 0.495

Gnomad AFR exome AF: 0.363

Gnomad AMR exome AF: 0.642

Gnomad ASJ exome AF: 0.435

Gnomad EAS exome AF: 0.349

Gnomad FIN exome AF: 0.453

Gnomad NFE exome AF: 0.503

Gnomad OTH exome AF: 0.495

GnomAD4 exome AF: 0.508 AC: 735890 AN: 1448570 Hom.: 188797 Cov.: 33 AF XY: 0.508 AC XY: 365813 AN XY: 720422

African (AFR) AF: 0.370 AC: 12144 AN: 32800

American (AMR) AF: 0.628 AC: 26795 AN: 42668

Ashkenazi Jewish (ASJ) AF: 0.431 AC: 10998 AN: 25516

East Asian (EAS) AF: 0.455 AC: 17892 AN: 39292

South Asian (SAS) AF: 0.529 AC: 44379 AN: 83846

European-Finnish (FIN) AF: 0.456 AC: 24167 AN: 53032

Middle Eastern (MID) AF: 0.459 AC: 2576 AN: 5610

European-Non Finnish (NFE) AF: 0.514 AC: 568043 AN: 1105966

Other (OTH) AF: 0.483 AC: 28896 AN: 59840

GnomAD4 genome AF: 0.464 AC: 70524 AN: 151986 Hom.: 16814 Cov.: 32 AF XY: 0.465 AC XY: 34525 AN XY: 74308

African (AFR) AF: 0.375 AC: 15560 AN: 41450

American (AMR) AF: 0.549 AC: 8374 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.424 AC: 1471 AN: 3470

East Asian (EAS) AF: 0.386 AC: 1998 AN: 5172

South Asian (SAS) AF: 0.541 AC: 2602 AN: 4814

European-Finnish (FIN) AF: 0.448 AC: 4735 AN: 10576

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.504 AC: 34233 AN: 67944

Other (OTH) AF: 0.455 AC: 959 AN: 2110

Alfa AF: 0.496 Hom.: 10706

Bravo AF: 0.465

Asia WGS AF: 0.469 AC: 1636 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	9.8
DANN	Benign	0.75
PhyloP100		0.62
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs1469000; hg19: chr7-23810605; COSMIC: COSV63457832;