rs2017047836

Variant names:

• chr17-41315502-C-A
• rs2017047836
• NM_031964.2:c.149G>T

Your query was ambiguous. Multiple possible variants found:

• chr17-41315502-C-A
• chr17-41315502-C-G
• chr17-41315502-C-T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_031964.2(KRTAP17-1):​c.149G>T​(p.Gly50Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 976,752 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 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. G50D) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 28)
  • Exomes 𝑓: 0.0000020 (0 hom.)
• Consequence: KRTAP17-1 NM_031964.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61
• Publications: 0 publications found

Genes affected

KRTAP17-1 (HGNC:18917): (keratin associated protein 17-1) This protein is a member of the keratin-associated protein (KAP) family. The KAP proteins form a matrix of keratin intermediate filaments which contribute to the structure of hair fibers. KAP family members appear to have unique, family-specific amino- and carboxyl-terminal regions and are subdivided into three multi-gene families according to amino acid composition: the high sulfur, the ultrahigh sulfur, and the high tyrosine/glycine KAPs. This protein is a member of the ultrahigh sulfur KAP family and the gene is localized to a cluster of KAPs at 17q12-q21. [provided by RefSeq, Jul 2008]

ENSG00000307895 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.091104).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_031964.2. 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
	KRTAP17-1	NM_031964.2	MANE Select	c.149G>T	p.Gly50Val	missense	Exon 1 of 1	NP_114170.1	Q9BYP8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KRTAP17-1	ENST00000334202.5	TSL:6 MANE Select	c.149G>T	p.Gly50Val	missense	Exon 1 of 1	ENSP00000333993.3	Q9BYP8
	ENSG00000307895	ENST00000829650.1		n.678+15046G>T		intron	N/A
	ENSG00000307895	ENST00000829651.1		n.333-12228G>T		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 28

GnomAD4 exome AF: 0.00000205 AC: 2 AN: 976752 Hom.: 0 Cov.: 28 AF XY: 0.00000205 AC XY: 1 AN XY: 486928

African (AFR) AF: 0.00 AC: 0 AN: 18116

American (AMR) AF: 0.00 AC: 0 AN: 32714

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 16836

East Asian (EAS) AF: 0.00 AC: 0 AN: 19360

South Asian (SAS) AF: 0.00 AC: 0 AN: 60586

European-Finnish (FIN) AF: 0.0000246 AC: 1 AN: 40572

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3476

European-Non Finnish (NFE) AF: 0.00000134 AC: 1 AN: 746012

Other (OTH) AF: 0.00 AC: 0 AN: 39080

GnomAD4 genome Cov.: 28

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.26
BayesDel_addAF	Benign	-0.11	T
BayesDel_noAF	Benign	-0.40
CADD	Benign	9.2
DANN	Benign	0.85
DEOGEN2	Benign	0.0032	T
Eigen	Benign	-0.69
Eigen_PC	Benign	-0.72
FATHMM_MKL	Benign	0.033	N
M_CAP	Benign	0.0077	T
MetaRNN	Benign	0.091	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Uncertain	2.1	M
PhyloP100		-1.6
PrimateAI	Benign	0.31	T
PROVEAN	Benign	-1.3	N
REVEL	Benign	0.031
Sift4G	Uncertain	0.021	D
Polyphen		0.40	B
Vest4		0.35
MutPred		0.25		Gain of sheet (P = 0.0043)
MVP		0.082
MPC		0.29
ClinPred		0.092	T
GERP RS		1.9
PromoterAI		0.012	Neutral
Varity_R		0.18
gMVP		0.049
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.16		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: rs2017047836; hg19: chr17-39471754;