chr17-41190230-G-A

Variant names:

• chr17-41190230-G-A
• rs749017430
• NM_001190460.1:c.344G>A

Variant summary

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

The NM_001190460.1(KRTAP9-1):​c.344G>A​(p.Cys115Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000641 in 1,248,376 control chromosomes in the GnomAD database, with no homozygous occurrence. 13/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 34)
  • Exomes 𝑓: 0.0000064 (0 hom.)
• Consequence: KRTAP9-1 NM_001190460.1 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.218
• Publications: 0 publications found

Genes affected

KRTAP9-1 (HGNC:18912): (keratin associated protein 9-1) Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001190460.1. 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
	KRTAP9-1	NM_001190460.1	MANE Select	c.344G>A	p.Cys115Tyr	missense	Exon 1 of 1	NP_001177389.1	A8MXZ3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KRTAP9-1	ENST00000398470.1	TSL:6 MANE Select	c.344G>A	p.Cys115Tyr	missense	Exon 1 of 1	ENSP00000381488.1	A8MXZ3

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD2 exomes AF: 0.00000818 AC: 2 AN: 244542 AF XY: 0.00000756

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.000111

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000641 AC: 8 AN: 1248376 Hom.: 0 Cov.: 134 AF XY: 0.00000811 AC XY: 5 AN XY: 616154

African (AFR) AF: 0.00 AC: 0 AN: 26822

American (AMR) AF: 0.00 AC: 0 AN: 28464

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 20200

East Asian (EAS) AF: 0.000277 AC: 8 AN: 28890

South Asian (SAS) AF: 0.00 AC: 0 AN: 64318

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 45122

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5030

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 979830

Other (OTH) AF: 0.00 AC: 0 AN: 49700

GnomAD4 genome Cov.: 34

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ExAC AF: 0.00000824 AC: 1

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.13
BayesDel_addAF	Benign	-0.32	T
BayesDel_noAF	Benign	-0.53
CADD	Benign	16
DANN	Benign	0.59
DEOGEN2	Benign	0.071	T
Eigen	Benign	-0.16
Eigen_PC	Benign	-0.26
FATHMM_MKL	Benign	0.43	N
LIST_S2	Benign	0.63	T
M_CAP	Benign	0.0015	T
MetaRNN	Uncertain	0.49	T
MetaSVM	Benign	-0.97	T
MutationAssessor	Uncertain	2.4	M
PhyloP100		0.22
PrimateAI	Benign	0.29	T
PROVEAN	Pathogenic	-4.9	D
REVEL	Benign	0.079
Sift	Uncertain	0.019	D
Sift4G	Benign	0.072	T
Vest4		0.21
MutPred		0.77		Gain of glycosylation at S113 (P = 0.1704)
MVP		0.16
MPC		0.039
ClinPred		0.45	T
GERP RS		1.5
PromoterAI		0.0040	Neutral
Varity_R		0.14
gMVP		0.13

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs749017430; hg19: chr17-39346482;