NM_007271.4:c.241A>C

Variant names:

• chr6-36524406-T-G
• rs56111125
• NM_007271.4:c.241A>C

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4_Moderate BP6_Moderate BP7 BS2

The NM_007271.4(STK38):​c.241A>C​(p.Arg81Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000665 in 1,613,614 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.0030 (2 hom., cov: 32)
  • Exomes 𝑓: 0.00042 (2 hom.)
• Consequence: STK38 NM_007271.4 synonymous
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 2.10
• Publications: 1 publications found

Genes affected

STK38 (HGNC:17847): (serine/threonine kinase 38) This gene encodes a member of the AGC serine/threonine kinase family of proteins. The kinase activity of this protein is regulated by autophosphorylation and phosphorylation by other upstream kinases. This protein has been shown to function in the cell cycle and apoptosis. This protein has also been found to regulate the protein stability and transcriptional activity of the MYC oncogene. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2015]

ACMG classification

Our verdict: Benign. The variant received -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.43).
• BP6: Variant 6-36524406-T-G is Benign according to our data. Variant chr6-36524406-T-G is described in ClinVar as Benign. ClinVar VariationId is 720945.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=2.1 with no splicing effect.
• BS2: High AC in GnomAd4 at 459 AD gene.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007271.4. 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
	STK38	NM_007271.4	MANE Select	c.241A>C	p.Arg81Arg	synonymous	Exon 4 of 14	NP_009202.1	Q15208
	STK38	NM_001305102.2		c.241A>C	p.Arg81Arg	synonymous	Exon 4 of 14	NP_001292031.1	Q15208

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STK38	ENST00000229812.8	TSL:1 MANE Select	c.241A>C	p.Arg81Arg	synonymous	Exon 4 of 14	ENSP00000229812.7	Q15208
	STK38	ENST00000869137.1		c.241A>C	p.Arg81Arg	synonymous	Exon 4 of 15	ENSP00000539196.1
	STK38	ENST00000850860.1		c.241A>C	p.Arg81Arg	synonymous	Exon 4 of 14	ENSP00000520947.1

Frequencies

GnomAD3 genomes AF: 0.00289 AC: 440 AN: 152216 Hom.: 1 Cov.: 32

Gnomad AFR AF: 0.00999

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000982

Gnomad ASJ AF: 0.000289

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000294

Gnomad OTH AF: 0.00383

GnomAD2 exomes AF: 0.000933 AC: 233 AN: 249794 AF XY: 0.000800

Gnomad AFR exome AF: 0.0115

Gnomad AMR exome AF: 0.000825

Gnomad ASJ exome AF: 0.000498

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000794

Gnomad OTH exome AF: 0.000329

GnomAD4 exome AF: 0.000420 AC: 614 AN: 1461280 Hom.: 2 Cov.: 30 AF XY: 0.000367 AC XY: 267 AN XY: 726894

African (AFR) AF: 0.0118 AC: 393 AN: 33446

American (AMR) AF: 0.000852 AC: 38 AN: 44612

Ashkenazi Jewish (ASJ) AF: 0.000727 AC: 19 AN: 26126

East Asian (EAS) AF: 0.00 AC: 0 AN: 39662

South Asian (SAS) AF: 0.0000348 AC: 3 AN: 86110

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53374

Middle Eastern (MID) AF: 0.000520 AC: 3 AN: 5764

European-Non Finnish (NFE) AF: 0.0000908 AC: 101 AN: 1111808

Other (OTH) AF: 0.000944 AC: 57 AN: 60378

GnomAD4 genome AF: 0.00301 AC: 459 AN: 152334 Hom.: 2 Cov.: 32 AF XY: 0.00318 AC XY: 237 AN XY: 74492

African (AFR) AF: 0.0104 AC: 432 AN: 41568

American (AMR) AF: 0.000980 AC: 15 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.000289 AC: 1 AN: 3466

East Asian (EAS) AF: 0.00 AC: 0 AN: 5184

South Asian (SAS) AF: 0.000207 AC: 1 AN: 4828

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10624

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0000294 AC: 2 AN: 68044

Other (OTH) AF: 0.00379 AC: 8 AN: 2112

Alfa AF: 0.00160 Hom.: 0

Bravo AF: 0.00363

Asia WGS AF: 0.00260 AC: 9 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
CADD	Benign	12
DANN	Benign	0.81
PhyloP100		2.1
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=98/2	polymorphism

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

Other links and lift over

dbSNP: rs56111125; hg19: chr6-36492183;