11-1584908-T-G

Position:

• chr11-1584908-T-G

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_Strong BP7

The NM_001005922.1(KRTAP5-1):​c.342A>C​(p.Gly114Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.029 (1 hom., cov: 0)
  • Exomes 𝑓: 0.011 (95 hom.)
  • Failed GnomAD Quality Control
• Consequence: KRTAP5-1 NM_001005922.1 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.04

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:):

ACMG classification

Verdict is Likely_benign. Variant got -5 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BP7: Synonymous conserved (PhyloP=-2.04 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KRTAP5-1	NM_001005922.1	c.342A>C	p.Gly114Gly	synonymous_variant	1/1	ENST00000382171.2	NP_001005922.1
KRTAP5-AS1	NR_021489.2	n.328+11840T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KRTAP5-1	ENST00000382171.2	c.342A>C	p.Gly114Gly	synonymous_variant	1/1	6	NM_001005922.1	ENSP00000371606.2

Frequencies

GnomAD3 genomes AF: 0.00 AC: 138 AN: 4630 Hom.: 1 Cov.: 0 FAILED QC

Gnomad AFR AF: 0.0246

Gnomad AMI AF: 0.0313

Gnomad AMR AF: 0.0110

Gnomad ASJ AF: 0.0250

Gnomad EAS AF: 0.0238

Gnomad SAS AF: 0.0143

Gnomad FIN AF: 0.0407

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0348

Gnomad OTH AF: 0.0500

GnomAD3 exomes AF: 0.0104 AC: 2089 AN: 200984 Hom.: 203 AF XY: 0.0105 AC XY: 1163 AN XY: 110790

Gnomad AFR exome AF: 0.00459

Gnomad AMR exome AF: 0.00980

Gnomad ASJ exome AF: 0.0154

Gnomad EAS exome AF: 0.00438

Gnomad SAS exome AF: 0.0146

Gnomad FIN exome AF: 0.00744

Gnomad NFE exome AF: 0.0111

Gnomad OTH exome AF: 0.0127

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0108 AC: 2695 AN: 249910 Hom.: 95 Cov.: 0 AF XY: 0.0108 AC XY: 1326 AN XY: 122298

Gnomad4 AFR exome AF: 0.0129

Gnomad4 AMR exome AF: 0.0139

Gnomad4 ASJ exome AF: 0.0116

Gnomad4 EAS exome AF: 0.00534

Gnomad4 SAS exome AF: 0.0109

Gnomad4 FIN exome AF: 0.0296

Gnomad4 NFE exome AF: 0.0102

Gnomad4 OTH exome AF: 0.0114

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0294 AC: 137 AN: 4654 Hom.: 1 Cov.: 0 AF XY: 0.0285 AC XY: 64 AN XY: 2246

Gnomad4 AFR AF: 0.0242

Gnomad4 AMR AF: 0.0109

Gnomad4 ASJ AF: 0.0250

Gnomad4 EAS AF: 0.0190

Gnomad4 SAS AF: 0.0139

Gnomad4 FIN AF: 0.0407

Gnomad4 NFE AF: 0.0348

Gnomad4 OTH AF: 0.0484

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.8
DANN	Benign	0.35

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: rs80025267; hg19: chr11-1606138; COSMIC: COSV66298770;