1-45353397-C-T

Variant names:

• chr1-45353397-C-T
• rs7544178
• NM_007170.3:c.540+1906G>A

Variant summary

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

The NM_007170.3(TESK2):​c.540+1906G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 152,114 control chromosomes in the GnomAD database, including 5,771 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 0.27 (5771 hom., cov: 32)
• Consequence: TESK2 NM_007170.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.28
• Publications: 2 publications found

Genes affected

TESK2 (HGNC:11732): (testis associated actin remodelling kinase 2) This gene product is a serine/threonine protein kinase that contains an N-terminal protein kinase domain that is structurally similar to the kinase domains of testis-specific protein kinase-1 and the LIM motif-containing protein kinases (LIMKs). Its overall structure is most related to the former, indicating that it belongs to the TESK subgroup of the LIMK/TESK family of protein kinases. This gene is predominantly expressed in testis and prostate. The developmental expression pattern of the rat gene in testis suggests an important role for this gene in meitoic stages and/or early stages of spermiogenesis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2016]

ENSG00000288208 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007170.3. 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
	TESK2	NM_007170.3	MANE Select	c.540+1906G>A		intron	N/A	NP_009101.2
	TESK2	NM_001320800.2		c.291+1906G>A		intron	N/A	NP_001307729.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TESK2	ENST00000372086.4	TSL:1 MANE Select	c.540+1906G>A		intron	N/A	ENSP00000361158.3
	TESK2	ENST00000372084.5	TSL:1	c.540+1906G>A		intron	N/A	ENSP00000361156.1
	ENSG00000288208	ENST00000671898.1		n.540+1906G>A		intron	N/A	ENSP00000499896.1

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40737 AN: 151996 Hom.: 5748 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.364

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.268 AC: 40785 AN: 152114 Hom.: 5771 Cov.: 32 AF XY: 0.267 AC XY: 19882 AN XY: 74380

African (AFR) AF: 0.267 AC: 11057 AN: 41470

American (AMR) AF: 0.404 AC: 6169 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.253 AC: 877 AN: 3472

East Asian (EAS) AF: 0.365 AC: 1889 AN: 5182

South Asian (SAS) AF: 0.232 AC: 1118 AN: 4824

European-Finnish (FIN) AF: 0.208 AC: 2203 AN: 10586

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.243 AC: 16507 AN: 67986

Other (OTH) AF: 0.302 AC: 637 AN: 2110

Alfa AF: 0.253 Hom.: 905

Bravo AF: 0.285

Asia WGS AF: 0.337 AC: 1172 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.19
PhyloP100		-2.3
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

Other links and lift over

dbSNP: rs7544178; hg19: chr1-45819069;