11-1607813-T-C

Position:

• chr11-1607813-T-C

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_Strong BP6_Moderate BP7

The NM_001012708.2(KRTAP5-3):​c.573A>G​(p.Lys191Lys) variant causes a synonymous 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 Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.00015 (0 hom., cov: 23)
  • Exomes 𝑓: 0.00015 (45 hom.)
  • Failed GnomAD Quality Control
• Consequence: KRTAP5-3 NM_001012708.2 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -3.76

Genes affected

KRTAP5-3 (HGNC:23598): (keratin associated protein 5-3) Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -7 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BP6: Variant 11-1607813-T-C is Benign according to our data. Variant chr11-1607813-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 2641348.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-3.76 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KRTAP5-3	NM_001012708.2	c.573A>G	p.Lys191Lys	synonymous_variant	1/1	ENST00000399685.1	NP_001012726.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KRTAP5-3	ENST00000399685.1	c.573A>G	p.Lys191Lys	synonymous_variant	1/1	6	NM_001012708.2	ENSP00000382592.1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 11 AN: 73274 Hom.: 0 Cov.: 23 FAILED QC

Gnomad AFR AF: 0.000315

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000142

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: 0.000116

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000152 AC: 210 AN: 1379810 Hom.: 45 Cov.: 134 AF XY: 0.000169 AC XY: 116 AN XY: 685064

Gnomad4 AFR exome AF: 0.0000622

Gnomad4 AMR exome AF: 0.000241

Gnomad4 ASJ exome AF: 0.000298

Gnomad4 EAS exome AF: 0.00123

Gnomad4 SAS exome AF: 0.000126

Gnomad4 FIN exome AF: 0.000272

Gnomad4 NFE exome AF: 0.000111

Gnomad4 OTH exome AF: 0.000144

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.000150 AC: 11 AN: 73284 Hom.: 0 Cov.: 23 AF XY: 0.0000830 AC XY: 3 AN XY: 36146

Gnomad4 AFR AF: 0.000314

Gnomad4 AMR AF: 0.000142

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000116

Gnomad4 OTH AF: 0.00

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Mar 01, 2023

KRTAP5-3: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.74
DANN	Benign	0.39

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

LitVar

Other links and lift over

dbSNP: rs12795274; hg19: chr11-1629043; COSMIC: COSV68790625;