7-43624878-T-C

Variant names:

• chr7-43624878-T-C
• rs15866
• NM_004760.3:c.*36T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 15 publications found

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]

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004760.3. 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
	STK17A	NM_004760.3	MANE Select	c.*36T>C		3_prime_UTR	Exon 7 of 7	NP_004751.2
	COA1	NR_135580.2		n.1407+6306A>G		intron	N/A
	COA1	NR_135581.2		n.808+14571A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STK17A	ENST00000319357.6	TSL:1 MANE Select	c.*36T>C		3_prime_UTR	Exon 7 of 7	ENSP00000319192.5
	STK17A	ENST00000474211.1	TSL:2	n.1961T>C		non_coding_transcript_exon	Exon 2 of 2
	STK17A	ENST00000648544.1		n.*36T>C		non_coding_transcript_exon	Exon 7 of 9	ENSP00000497301.1

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

GnomAD2 exomes AF: 0.519 AC: 99084 AN: 190918 AF XY: 0.515

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 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

African (AFR) AF: 0.816 AC: 24845 AN: 30450

American (AMR) AF: 0.537 AC: 18121 AN: 33766

Ashkenazi Jewish (ASJ) AF: 0.509 AC: 11081 AN: 21754

East Asian (EAS) AF: 0.578 AC: 22547 AN: 38990

South Asian (SAS) AF: 0.644 AC: 46568 AN: 72344

European-Finnish (FIN) AF: 0.448 AC: 21923 AN: 48982

Middle Eastern (MID) AF: 0.578 AC: 2797 AN: 4840

European-Non Finnish (NFE) AF: 0.434 AC: 460015 AN: 1059448

Other (OTH) AF: 0.504 AC: 28485 AN: 56472

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

African (AFR) AF: 0.796 AC: 33001 AN: 41452

American (AMR) AF: 0.535 AC: 8161 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.512 AC: 1778 AN: 3470

East Asian (EAS) AF: 0.583 AC: 3013 AN: 5170

South Asian (SAS) AF: 0.647 AC: 3119 AN: 4820

European-Finnish (FIN) AF: 0.435 AC: 4580 AN: 10526

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.440 AC: 29905 AN: 67974

Other (OTH) AF: 0.533 AC: 1126 AN: 2112

Alfa AF: 0.505 Hom.: 10979

Bravo AF: 0.576

Asia WGS AF: 0.599 AC: 2080 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	11
DANN	Benign	0.84
PhyloP100		0.17
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: rs15866; hg19: chr7-43664477; COSMIC: COSV60046819;