dbSNP rs768468038: KRTAP5-2:p.Gly86Trp (chr11-1597995-C-A) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_001004325.2(KRTAP5-2):c.256G>T(p.Gly86Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.0 ( 0 hom., cov: 13)

Exomes 𝑓: 0.0000034 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

KRTAP5-2
NM_001004325.2 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.336

Publications

0 publications found

Variant links:

Genes affected

KRTAP5-2 (HGNC:23597): (keratin associated protein 5-2) Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

KRTAP5-2 links:

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

KRTAP5-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.21662635).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001004325.2. 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
	KRTAP5-2	NM_001004325.2	MANE Select	c.256G>T	p.Gly86Trp	missense	Exon 1 of 1	NP_001004325.1	Q701N4
	KRTAP5-AS1	NR_021489.2		n.1076C>A		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
KRTAP5-2	ENST00000412090.2	TSL:6 MANE Select	c.256G>T	p.Gly86Trp	missense	Exon 1 of 1	ENSP00000400041.1	Q701N4
KRTAP5-AS1	ENST00000424148.1	TSL:2	n.1076C>A		non_coding_transcript_exon	Exon 2 of 2
KRTAP5-AS1	ENST00000792906.1		n.214-14370C>A		intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

66388

Hom.:

Cov.:

Gnomad AFR

AF:

0.00

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

GnomAD2 exomes

AF:

0.00000933

AC:

AN:

214312

AF XY:

0.00

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000202

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00000340

AC:

AN:

1176706

Hom.:

Cov.:

AF XY:

0.00000171

AC XY:

AN XY:

583902

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

25814

American (AMR)

AF:

0.00

AC:

AN:

36138

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

19894

East Asian (EAS)

AF:

0.00

AC:

AN:

25428

South Asian (SAS)

AF:

0.00

AC:

AN:

70400

European-Finnish (FIN)

AF:

0.00

AC:

AN:

32102

Middle Eastern (MID)

AF:

0.00

AC:

AN:

3492

European-Non Finnish (NFE)

AF:

0.00000436

AC:

AN:

917820

Other (OTH)

AF:

0.00

AC:

AN:

45618

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

66510

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

32182

African (AFR)

AF:

0.00

AC:

AN:

18164

American (AMR)

AF:

0.00

AC:

AN:

7178

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

1888

East Asian (EAS)

AF:

0.00

AC:

AN:

2618

South Asian (SAS)

AF:

0.00

AC:

AN:

2126

European-Finnish (FIN)

AF:

0.00

AC:

AN:

3500

Middle Eastern (MID)

AF:

0.00

AC:

AN:

126

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

29598

Other (OTH)

AF:

0.00

AC:

AN:

978

Alfa

AF:

0.0000312

Hom.:

ExAC

AF:

0.00000828

AC:

ClinVar

ClinVar submissions

Significance:Uncertain significance

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.30

BayesDel_addAF

Benign

-0.18

BayesDel_noAF

Benign

-0.50

CADD

Benign

(source)

DANN

Benign

0.77

DEOGEN2

Benign

0.091

Eigen

Benign

-0.028

Eigen_PC

Benign

-0.28

FATHMM_MKL

Benign

0.012

M_CAP

Benign

0.0091

MetaRNN

Benign

0.22

MetaSVM

Benign

-1.1

MutationAssessor

Pathogenic

3.6

PhyloP100

-0.34

PROVEAN

Benign

-1.3

REVEL

Benign

0.087

Sift4G

Uncertain

0.0050

Polyphen

1.0

Vest4

0.39

MutPred

0.32

Loss of phosphorylation at S84 (P = 0.1218)

MVP

0.076

MPC

0.10

ClinPred

0.37

GERP RS

2.9

PromoterAI

-0.014

Neutral

(source)

Varity_R

0.24

gMVP

0.058

Mutation Taster

=100/0

polymorphism

(source)

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over