7-43625186-C-T

Position:

• chr7-43625186-C-T

Variant summary

Our verdict is Benign. Variant got -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

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:):

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=-0.68).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.831 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STK17A	NM_004760.3	c.*344C>T		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.*344C>T		3_prime_UTR_variant	7/7	1	NM_004760.3	ENSP00000319192.5

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

Gnomad4 AFR exome AF: 0.825

Gnomad4 AMR exome AF: 0.617

Gnomad4 ASJ exome AF: 0.692

Gnomad4 EAS exome AF: 0.563

Gnomad4 SAS exome AF: 0.755

Gnomad4 FIN exome AF: 0.671

Gnomad4 NFE exome AF: 0.643

Gnomad4 OTH exome AF: 0.662

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

Gnomad4 AFR AF: 0.838

Gnomad4 AMR AF: 0.663

Gnomad4 ASJ AF: 0.693

Gnomad4 EAS AF: 0.589

Gnomad4 SAS AF: 0.760

Gnomad4 FIN AF: 0.664

Gnomad4 NFE AF: 0.655

Gnomad4 OTH AF: 0.676

Alfa AF: 0.662 Hom.: 10850

Bravo AF: 0.709

Asia WGS AF: 0.658 AC: 2288 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	6.4
DANN	Benign	0.75

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: rs1044217; hg19: chr7-43664785;