17-15999897-G-T

Variant names:

• chr17-15999897-G-T
• rs1970661570
• NM_017775.4:c.49G>T

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2 BP4

The NM_017775.4(TTC19):​c.49G>T​(p.Ala17Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000803 in 1,245,370 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A17T) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 8.0e-7 (0 hom.)
• Consequence: TTC19 NM_017775.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.277
• Publications: 0 publications found

Genes affected

TTC19 (HGNC:26006): (tetratricopeptide repeat domain 19) This gene encodes a protein with a tetratricopeptide repeat (TPR) domain containing several TPRs of about 34 aa each. These repeats are found in a variety of organisms including bacteria, fungi and plants, and are involved in a variety of functions including protein-protein interactions. This protein is embedded in the inner mitochondrial membrane and is involved in the formation of the mitochondrial respiratory chain III. It has also been suggested that this protein plays a role in cytokinesis. Mutations in this gene cause mitochondrial complex III deficiency. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Sep 2012]

ZSWIM7 (HGNC:26993): (zinc finger SWIM-type containing 7) Predicted to enable zinc ion binding activity. Involved in double-strand break repair via homologous recombination and protein stabilization. Part of Shu complex. [provided by Alliance of Genome Resources, Apr 2022]

ZSWIM7 Gene-Disease associations (from GenCC):

• male infertility with azoospermia or oligozoospermia due to single gene mutation

  Inheritance: AR Classification: STRONG Submitted by: King Faisal Specialist Hospital and Research Center
• ovarian dysgenesis 10

  Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
• colorectal adenoma

  Inheritance: Unknown Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.28630418).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017775.4. 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
	TTC19	NM_017775.4	MANE Select	c.49G>T	p.Ala17Ser	missense	Exon 1 of 10	NP_060245.3
	TTC19	NM_001271420.2		c.-410G>T		5_prime_UTR	Exon 1 of 10	NP_001258349.1
	ZSWIM7	NM_001042697.2	MANE Select	c.-303C>A		upstream_gene	N/A	NP_001036162.1	Q19AV6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TTC19	ENST00000261647.10	TSL:1 MANE Select	c.49G>T	p.Ala17Ser	missense	Exon 1 of 10	ENSP00000261647.5	Q6DKK2
	TTC19	ENST00000873205.1		c.49G>T	p.Ala17Ser	missense	Exon 1 of 10	ENSP00000543264.1
	TTC19	ENST00000873204.1		c.49G>T	p.Ala17Ser	missense	Exon 1 of 10	ENSP00000543263.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 8.03e-7 AC: 1 AN: 1245370 Hom.: 0 Cov.: 30 AF XY: 0.00000165 AC XY: 1 AN XY: 605092

African (AFR) AF: 0.00 AC: 0 AN: 24336

American (AMR) AF: 0.00 AC: 0 AN: 14448

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 17558

East Asian (EAS) AF: 0.00 AC: 0 AN: 28808

South Asian (SAS) AF: 0.00 AC: 0 AN: 58116

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 29740

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3546

European-Non Finnish (NFE) AF: 9.83e-7 AC: 1 AN: 1017398

Other (OTH) AF: 0.00 AC: 0 AN: 51420

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.12
BayesDel_addAF	Benign	-0.011	T
BayesDel_noAF	Benign	-0.25
CADD	Benign	13
DANN	Benign	0.82
DEOGEN2	Benign	0.0051	T
Eigen	Benign	-0.47
Eigen_PC	Benign	-0.56
FATHMM_MKL	Benign	0.26	N
LIST_S2	Benign	0.55	T
M_CAP	Pathogenic	0.89	D
MetaRNN	Benign	0.29	T
MetaSVM	Uncertain	-0.27	T
MutationAssessor	Benign	0.81	L
PhyloP100		0.28
PrimateAI	Uncertain	0.77	T
PROVEAN	Benign	-0.43	N
REVEL	Benign	0.14
Sift	Benign	0.032	D
Sift4G	Pathogenic	0.0	D
Vest4		0.32
MutPred		0.34		Gain of phosphorylation at A17 (P = 0.0037)
MVP		0.79
MPC		0.12
ClinPred		0.10	T
GERP RS		3.2
PromoterAI		0.058	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		2.8
Varity_R		0.062
gMVP		0.36

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: rs1970661570; hg19: chr17-15903211;