rs7805969

chr7-43611448-A-Gchr7-43611448-A-T

Variant summary

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

The NM_004760.3(STK17A):c.564+3048A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.588 in 152,048 control chromosomes in the GnomAD database, including 26,492 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 0.59 (26492 hom., cov: 32)
• Consequence: STK17A NM_004760.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.163

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.625 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STK17A	NM_004760.3	c.564+3048A>G		intron_variant		ENST00000319357.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STK17A	ENST00000319357.6	c.564+3048A>G		intron_variant		1	NM_004760.3	P1

Frequencies

GnomAD3 genomes AF: 0.588 AC: 89375 AN: 151930 Hom.: 26467 Cov.: 32

Gnomad AFR AF: 0.517

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.619

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.620

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.612

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.630

Gnomad OTH AF: 0.597

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

GnomAD4 genome AF: 0.588 AC: 89449 AN: 152048 Hom.: 26492 Cov.: 32 AF XY: 0.587 AC XY: 43645 AN XY: 74350

Gnomad4 AFR AF: 0.517

Gnomad4 AMR AF: 0.619

Gnomad4 ASJ AF: 0.537

Gnomad4 EAS AF: 0.618

Gnomad4 SAS AF: 0.462

Gnomad4 FIN AF: 0.612

Gnomad4 NFE AF: 0.630

Gnomad4 OTH AF: 0.598

Alfa AF: 0.600 Hom.: 3982

Bravo AF: 0.588

Asia WGS AF: 0.548 AC: 1904 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	3.4
Dann	Benign	0.53

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: rs7805969; hg19: chr7-43651047;