11-1584931-C-G

Position:

• chr11-1584931-C-G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_001005922.1(KRTAP5-1):​c.319G>C​(p.Gly107Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 8)
  • Exomes 𝑓: 0.000024 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: KRTAP5-1 NM_001005922.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02

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.

• BP4: Computational evidence support a benign effect (MetaRNN=0.13535509).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KRTAP5-1	NM_001005922.1	c.319G>C	p.Gly107Arg	missense_variant	1/1	ENST00000382171.2
KRTAP5-AS1	NR_021489.2	n.328+11863C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KRTAP5-1	ENST00000382171.2	c.319G>C	p.Gly107Arg	missense_variant	1/1		NM_001005922.1	P1
KRTAP5-AS1	ENST00000424148.1	n.328+11863C>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes Cov.: 8

GnomAD3 exomes AF: 0.0000730 AC: 17 AN: 232816 Hom.: 1 AF XY: 0.0000869 AC XY: 11 AN XY: 126570

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.0000629

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000488

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00000959

Gnomad OTH exome AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000240 AC: 29 AN: 1207372 Hom.: 0 Cov.: 48 AF XY: 0.0000334 AC XY: 20 AN XY: 598186

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0000284

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000345

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000106

Gnomad4 OTH exome AF: 0.0000439

GnomAD4 genome Cov.: 8

ExAC AF: 0.0000662 AC: 8

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.40
BayesDel_addAF	Benign	-0.46	T
BayesDel_noAF	Benign	-0.57
CADD	Benign	11
DANN	Benign	0.47
DEOGEN2	Benign	0.096	T
Eigen	Benign	-0.65
Eigen_PC	Benign	-0.90
FATHMM_MKL	Benign	0.020	N
M_CAP	Benign	0.00082	T
MetaRNN	Benign	0.14	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Uncertain	2.2	M
MutationTaster	Benign	1.0	N
PROVEAN	Uncertain	-3.8	D
REVEL	Benign	0.063
Sift	Pathogenic	0.0	D
Sift4G	Uncertain	0.056	T
Polyphen		0.96	D
Vest4		0.44
MutPred		0.22		Loss of glycosylation at S105 (P = 0.0857);
MVP		0.17
MPC		0.047
ClinPred		0.23	T
GERP RS		-0.20
Varity_R		0.20
gMVP		0.027

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: rs778910407; hg19: chr11-1606161;