chr7-23762384-A-G

Position:

• chr7-23762384-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_031414.5(STK31):​c.1294-417A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.751 in 151,986 control chromosomes in the GnomAD database, including 43,039 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 0.75 (43039 hom., cov: 31)
• Consequence: STK31 NM_031414.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.359

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.805 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STK31	NM_031414.5	c.1294-417A>G		intron_variant		ENST00000355870.8	NP_113602.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STK31	ENST00000355870.8	c.1294-417A>G		intron_variant		1	NM_031414.5	ENSP00000348132	P4

Frequencies

GnomAD3 genomes AF: 0.751 AC: 114039 AN: 151868 Hom.: 43020 Cov.: 31

Gnomad AFR AF: 0.783

Gnomad AMI AF: 0.771

Gnomad AMR AF: 0.761

Gnomad ASJ AF: 0.682

Gnomad EAS AF: 0.826

Gnomad SAS AF: 0.812

Gnomad FIN AF: 0.796

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.717

Gnomad OTH AF: 0.723

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

GnomAD4 genome AF: 0.751 AC: 114110 AN: 151986 Hom.: 43039 Cov.: 31 AF XY: 0.757 AC XY: 56244 AN XY: 74290

Gnomad4 AFR AF: 0.783

Gnomad4 AMR AF: 0.761

Gnomad4 ASJ AF: 0.682

Gnomad4 EAS AF: 0.826

Gnomad4 SAS AF: 0.809

Gnomad4 FIN AF: 0.796

Gnomad4 NFE AF: 0.717

Gnomad4 OTH AF: 0.727

Alfa AF: 0.716 Hom.: 50373

Bravo AF: 0.749

Asia WGS AF: 0.813 AC: 2824 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.44
DANN	Benign	0.66

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs10278268; hg19: chr7-23802003;