rs10278268

Variant names:

• chr7-23762384-A-G
• rs10278268
• NM_031414.5:c.1294-417A>G

Your query was ambiguous. Multiple possible variants found:

• chr7-23762384-A-G
• chr7-23762384-A-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.805 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STK31	NM_031414.5	MANE Select	c.1294-417A>G		intron	N/A	NP_113602.2
	STK31	NM_001260504.2		c.1225-417A>G		intron	N/A	NP_001247433.1	A0A140VKG1
	STK31	NM_001260505.2		c.1294-417A>G		intron	N/A	NP_001247434.1	Q9BXU1-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STK31	ENST00000355870.8	TSL:1 MANE Select	c.1294-417A>G		intron	N/A	ENSP00000348132.3	Q9BXU1-1
	STK31	ENST00000354639.7	TSL:1	c.1225-417A>G		intron	N/A	ENSP00000346660.3	Q9BXU1-2
	STK31	ENST00000405627.7	TSL:1	n.1819-417A>G		intron	N/A

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

African (AFR) AF: 0.783 AC: 32436 AN: 41442

American (AMR) AF: 0.761 AC: 11615 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.682 AC: 2366 AN: 3470

East Asian (EAS) AF: 0.826 AC: 4267 AN: 5168

South Asian (SAS) AF: 0.809 AC: 3902 AN: 4824

European-Finnish (FIN) AF: 0.796 AC: 8378 AN: 10526

Middle Eastern (MID) AF: 0.684 AC: 201 AN: 294

European-Non Finnish (NFE) AF: 0.717 AC: 48712 AN: 67982

Other (OTH) AF: 0.727 AC: 1530 AN: 2104

Alfa AF: 0.722 Hom.: 71901

Bravo AF: 0.749

Asia WGS AF: 0.813 AC: 2824 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.44
DANN	Benign	0.66
PhyloP100		-0.36
Mutation Taster		=100/0	polymorphism (auto)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10278268;

hg19: chr7-23802003;