11-71582800-C-A

Position:

• chr11-71582800-C-A

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001005405.3(KRTAP5-11):​c.38G>T​(p.Gly13Val) variant causes a missense 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. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: KRTAP5-11 NM_001005405.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.622

Genes affected

KRTAP5-11 (HGNC:23606): (keratin associated protein 5-11) Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

KRTAP5-11 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.1172221).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KRTAP5-11	NM_001005405.3	c.38G>T	p.Gly13Val	missense_variant	1/1	ENST00000398530.1	NP_001005405.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KRTAP5-11	ENST00000398530.1	c.38G>T	p.Gly13Val	missense_variant	1/1	6	NM_001005405.3	ENSP00000381541.1
KRTAP5-11	ENST00000526239.1	n.381-643G>T		intron_variant		5

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Jul 13, 2022

The c.38G>T (p.G13V) alteration is located in exon 1 (coding exon 1) of the KRTAP5-11 gene. This alteration results from a G to T substitution at nucleotide position 38, causing the glycine (G) at amino acid position 13 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.13
BayesDel_addAF	Benign	-0.24	T
BayesDel_noAF	Benign	-0.58
CADD	Benign	8.4
DANN	Benign	0.80
DEOGEN2	Benign	0.035	.;T
Eigen	Benign	-0.55
Eigen_PC	Benign	-0.54
FATHMM_MKL	Benign	0.44	N
LIST_S2	Benign	0.29	T;T
M_CAP	Benign	0.0038	T
MetaRNN	Benign	0.12	T;T
MetaSVM	Benign	-0.87	T
MutationAssessor	Uncertain	2.2	.;M
PROVEAN	Benign	2.2	.;N
REVEL	Benign	0.11
Sift	Pathogenic	0.0	.;D
Sift4G	Benign	0.32	T;T
Polyphen		0.024	.;B
Vest4		0.21
MutPred		0.20		Loss of glycosylation at S12 (P = 0.0339);Loss of glycosylation at S12 (P = 0.0339);
MVP		0.10
MPC		0.011
ClinPred		0.20	T
GERP RS		1.3
Varity_R		0.073
gMVP		0.029

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr11-71293846;