chr7-43625186-C-T

Variant names:

• chr7-43625186-C-T
• rs1044217
• NM_004760.3:c.*344C>T

Variant summary

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

The NM_004760.3(STK17A):​c.*344C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.698 in 189,902 control chromosomes in the GnomAD database, including 46,933 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 0.71 (38677 hom., cov: 32)
  • Exomes 𝑓: 0.65 (8256 hom.)
• Consequence: STK17A NM_004760.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.385
• Publications: 11 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=-0.68).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.831 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STK17A	NM_004760.3	MANE Select	c.*344C>T		3_prime_UTR	Exon 7 of 7	NP_004751.2	Q9UEE5
	COA1	NR_135580.2		n.1407+5998G>A		intron	N/A
	COA1	NR_135581.2		n.808+14263G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STK17A	ENST00000319357.6	TSL:1 MANE Select	c.*344C>T		3_prime_UTR	Exon 7 of 7	ENSP00000319192.5	Q9UEE5
	STK17A	ENST00000869874.1		c.*344C>T		3_prime_UTR	Exon 6 of 6	ENSP00000539933.1
	COA1	ENST00000415076.6	TSL:3	n.*133+14263G>A		intron	N/A	ENSP00000400759.1	Q9GZY4

Frequencies

GnomAD3 genomes AF: 0.708 AC: 107681 AN: 152028 Hom.: 38640 Cov.: 32

Gnomad AFR AF: 0.838

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.663

Gnomad ASJ AF: 0.693

Gnomad EAS AF: 0.588

Gnomad SAS AF: 0.760

Gnomad FIN AF: 0.664

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.655

Gnomad OTH AF: 0.678

GnomAD4 exome AF: 0.655 AC: 24726 AN: 37756 Hom.: 8256 Cov.: 0 AF XY: 0.658 AC XY: 12618 AN XY: 19184

African (AFR) AF: 0.825 AC: 713 AN: 864

American (AMR) AF: 0.617 AC: 1598 AN: 2588

Ashkenazi Jewish (ASJ) AF: 0.692 AC: 852 AN: 1232

East Asian (EAS) AF: 0.563 AC: 1184 AN: 2104

South Asian (SAS) AF: 0.755 AC: 2444 AN: 3238

European-Finnish (FIN) AF: 0.671 AC: 929 AN: 1384

Middle Eastern (MID) AF: 0.783 AC: 130 AN: 166

European-Non Finnish (NFE) AF: 0.643 AC: 15349 AN: 23872

Other (OTH) AF: 0.662 AC: 1527 AN: 2308

GnomAD4 genome AF: 0.708 AC: 107780 AN: 152146 Hom.: 38677 Cov.: 32 AF XY: 0.706 AC XY: 52521 AN XY: 74376

African (AFR) AF: 0.838 AC: 34820 AN: 41536

American (AMR) AF: 0.663 AC: 10135 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.693 AC: 2404 AN: 3468

East Asian (EAS) AF: 0.589 AC: 3049 AN: 5176

South Asian (SAS) AF: 0.760 AC: 3672 AN: 4830

European-Finnish (FIN) AF: 0.664 AC: 7008 AN: 10554

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.655 AC: 44525 AN: 67974

Other (OTH) AF: 0.676 AC: 1428 AN: 2112

Alfa AF: 0.670 Hom.: 12335

Bravo AF: 0.709

Asia WGS AF: 0.658 AC: 2288 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	6.4
DANN	Benign	0.75
PhyloP100		-0.39
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: rs1044217; hg19: chr7-43664785;