7-43624878-T-C

Position:

• chr7-43624878-T-C

Variant summary

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

The NM_004760.3(STK17A):​c.*36T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.475 in 1,519,036 control chromosomes in the GnomAD database, including 179,036 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 0.56 (25723 hom., cov: 32)
  • Exomes 𝑓: 0.47 (153313 hom.)
• Consequence: STK17A NM_004760.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.170

Genes affected

STK17A (HGNC:11395): (serine/threonine kinase 17a) This gene is a member of the DAP kinase-related apoptosis-inducing protein kinase family and encodes an autophosphorylated nuclear protein with a protein kinase domain. The protein has apoptosis-inducing activity. [provided by RefSeq, Jul 2008]

STK17A (HGNC:):

COA1 (HGNC:21868): (cytochrome c oxidase assembly factor 1) Involved in mitochondrial cytochrome c oxidase assembly and mitochondrial respiratory chain complex I assembly. Located in cytosol and mitochondrion. Is integral component of mitochondrial inner membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.789 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STK17A	NM_004760.3	c.*36T>C		3_prime_UTR_variant	7/7	ENST00000319357.6	NP_004751.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STK17A	ENST00000319357.6	c.*36T>C		3_prime_UTR_variant	7/7	1	NM_004760.3	ENSP00000319192.5

Frequencies

GnomAD3 genomes AF: 0.561 AC: 85216 AN: 151872 Hom.: 25679 Cov.: 32

Gnomad AFR AF: 0.796

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.646

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.533

GnomAD3 exomes AF: 0.519 AC: 99084 AN: 190918 Hom.: 26563 AF XY: 0.515 AC XY: 52892 AN XY: 102748

Gnomad AFR exome AF: 0.805

Gnomad AMR exome AF: 0.538

Gnomad ASJ exome AF: 0.517

Gnomad EAS exome AF: 0.591

Gnomad SAS exome AF: 0.640

Gnomad FIN exome AF: 0.446

Gnomad NFE exome AF: 0.447

Gnomad OTH exome AF: 0.506

GnomAD4 exome AF: 0.466 AC: 636382 AN: 1367046 Hom.: 153313 Cov.: 23 AF XY: 0.469 AC XY: 316983 AN XY: 675522

Gnomad4 AFR exome AF: 0.816

Gnomad4 AMR exome AF: 0.537

Gnomad4 ASJ exome AF: 0.509

Gnomad4 EAS exome AF: 0.578

Gnomad4 SAS exome AF: 0.644

Gnomad4 FIN exome AF: 0.448

Gnomad4 NFE exome AF: 0.434

Gnomad4 OTH exome AF: 0.504

GnomAD4 genome AF: 0.561 AC: 85325 AN: 151990 Hom.: 25723 Cov.: 32 AF XY: 0.563 AC XY: 41794 AN XY: 74270

Gnomad4 AFR AF: 0.796

Gnomad4 AMR AF: 0.535

Gnomad4 ASJ AF: 0.512

Gnomad4 EAS AF: 0.583

Gnomad4 SAS AF: 0.647

Gnomad4 FIN AF: 0.435

Gnomad4 NFE AF: 0.440

Gnomad4 OTH AF: 0.533

Alfa AF: 0.502 Hom.: 7462

Bravo AF: 0.576

Asia WGS AF: 0.599 AC: 2080 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	11
DANN	Benign	0.84

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: rs15866; hg19: chr7-43664477; COSMIC: COSV60046819;