7-43624878-T-A

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_004760.3(STK17A):​c.*36T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).

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>A		3_prime_UTR	Exon 7 of 7	NP_004751.2
	COA1	NR_135580.2		n.1407+6306A>T		intron	N/A
	COA1	NR_135581.2		n.808+14571A>T		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>A		3_prime_UTR	Exon 7 of 7	ENSP00000319192.5
	STK17A	ENST00000474211.1	TSL:2	n.1961T>A		non_coding_transcript_exon	Exon 2 of 2
	STK17A	ENST00000648544.1		n.*36T>A		non_coding_transcript_exon	Exon 7 of 9	ENSP00000497301.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 1368928 Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0 AN XY: 676460

African (AFR) AF: 0.00 AC: 0 AN: 30466

American (AMR) AF: 0.00 AC: 0 AN: 33796

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 21770

East Asian (EAS) AF: 0.00 AC: 0 AN: 39012

South Asian (SAS) AF: 0.00 AC: 0 AN: 72410

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 49048

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4844

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1061048

Other (OTH) AF: 0.00 AC: 0 AN: 56534

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 10979

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	10
DANN	Benign	0.85
PhyloP100		0.17

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;