rs199544345

Variant names:

• chr11-1584652-C-A
• rs199544345
• NM_001005922.1:c.598G>T

Your query was ambiguous. Multiple possible variants found:

• chr11-1584652-C-A
• chr11-1584652-C-G
• chr11-1584652-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001005922.1(KRTAP5-1):​c.598G>T​(p.Gly200Cys) 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. 14/20 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. G200S) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.0000093 (0 hom., cov: 27)
  • Failed GnomAD Quality Control
• Consequence: KRTAP5-1 NM_001005922.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.04

Genes affected

KRTAP5-1 (HGNC:23596): (keratin associated protein 5-1) Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

KRTAP5-AS1 (HGNC:27877): (KRTAP5-1/KRTAP5-2 antisense RNA 1)

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.048812985).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KRTAP5-1	NM_001005922.1	c.598G>T	p.Gly200Cys	missense_variant	Exon 1 of 1	ENST00000382171.2	NP_001005922.1
KRTAP5-AS1	NR_021489.2	n.328+11584C>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KRTAP5-1	ENST00000382171.2	c.598G>T	p.Gly200Cys	missense_variant	Exon 1 of 1	6	NM_001005922.1	ENSP00000371606.2

Frequencies

GnomAD3 genomes AF: 0.00 AC: 1 AN: 107640 Hom.: 0 Cov.: 27 FAILED QC

Gnomad AFR AF: 0.0000344

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Cov.: 31

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000929 AC: 1 AN: 107640 Hom.: 0 Cov.: 27 AF XY: 0.0000192 AC XY: 1 AN XY: 52154

Gnomad4 AFR AF: 0.0000344

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.091
BayesDel_addAF	Benign	-0.29	T
BayesDel_noAF	Benign	-0.65
CADD	Benign	0.64
DANN	Benign	0.66
DEOGEN2	Benign	0.0021	T
Eigen	Benign	-2.2
Eigen_PC	Benign	-2.3
FATHMM_MKL	Benign	0.00029	N
M_CAP	Benign	0.0022	T
MetaRNN	Benign	0.049	T
MetaSVM	Benign	-0.96	T
MutationAssessor	Benign	1.7	L
PROVEAN	Benign	2.0	N
REVEL	Benign	0.049
Sift	Pathogenic	0.0	D
Sift4G	Benign	0.25	T
Polyphen		0.0040	B
Vest4		0.17
MutPred		0.19		Loss of glycosylation at S199 (P = 0.032);
MVP		0.067
MPC		0.043
ClinPred		0.066	T
GERP RS		-5.4
Varity_R		0.14
gMVP		0.018

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

Publications

LitVar

Other links and lift over

dbSNP: rs199544345; hg19: chr11-1605882;