rs1044217

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr7-43625186-C-G
• chr7-43625186-C-T

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.*344C>G 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: -0.385
• 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: 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=-0.65).

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>G		3_prime_UTR	Exon 7 of 7	NP_004751.2	Q9UEE5
	COA1	NR_135580.2		n.1407+5998G>C		intron	N/A
	COA1	NR_135581.2		n.808+14263G>C		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>G		3_prime_UTR	Exon 7 of 7	ENSP00000319192.5	Q9UEE5
	STK17A	ENST00000869874.1		c.*344C>G		3_prime_UTR	Exon 6 of 6	ENSP00000539933.1
	COA1	ENST00000415076.6	TSL:3	n.*133+14263G>C		intron	N/A	ENSP00000400759.1	Q9GZY4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 37904 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 19262

African (AFR) AF: 0.00 AC: 0 AN: 866

American (AMR) AF: 0.00 AC: 0 AN: 2598

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 1240

East Asian (EAS) AF: 0.00 AC: 0 AN: 2118

South Asian (SAS) AF: 0.00 AC: 0 AN: 3246

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 1394

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 166

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 23960

Other (OTH) AF: 0.00 AC: 0 AN: 2316

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 12335

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	6.0
DANN	Benign	0.83
PhyloP100		-0.39

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;