Variant 17-41034721-C-CAGCTGGTCTCACAGCAGCTTGGCTGGCAGG details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM4BP6_ModerateBA1

The NM_030966.2(KRTAP1-3):c.100_101insCCTGCCAGCCAAGCTGCTGTGAGACCAGCT(p.Ser33_Cys34insSerCysGlnProSerCysCysGluThrSer) variant causes a conservative inframe insertion change. The variant allele was found at a frequency of 0.0309 in 142,046 control chromosomes in the GnomAD database, including 435 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.031 ( 435 hom., cov: 32)

Exomes 𝑓: 0.011 ( 900 hom. )

Failed GnomAD Quality Control

Consequence

KRTAP1-3
NM_030966.2 conservative_inframe_insertion

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 4.10

Variant links:

Genes affected

KRTAP1-3 (HGNC:16771): (keratin associated protein 1-3) This protein is a member of the keratin-associated protein (KAP) family. The KAP proteins form a matrix of keratin intermediate filaments which contribute to the structure of hair fibers. KAP family members appear to have unique, family-specific amino- and carboxyl-terminal regions and are subdivided into three multi-gene families according to amino acid composition: the high sulfur, the ultrahigh sulfur, and the high tyrosine/glycine KAPs. This protein is a member of the high sulfur KAP family and the gene is localized to a cluster of KAPs at 17q12-q21. [provided by RefSeq, Jul 2008]

KRTAP1-3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

PM4

Nonframeshift variant in NON repetitive region in NM_030966.2.

BP6

Variant 17-41034721-C-CAGCTGGTCTCACAGCAGCTTGGCTGGCAGG is Benign according to our data. Variant chr17-41034721-C-CAGCTGGTCTCACAGCAGCTTGGCTGGCAGG is described in ClinVar as [Benign]. Clinvar id is 768882.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0798 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KRTAP1-3	NM_030966.2 linkuse as main transcript	c.100_101insCCTGCCAGCCAAGCTGCTGTGAGACCAGCT	p.Ser33_Cys34insSerCysGlnProSerCysCysGluThrSer	conservative_inframe_insertion	1/1	ENST00000344363.7	NP_112228.1	Q8IUG1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KRTAP1-3	ENST00000344363.7 linkuse as main transcript	c.100_101insCCTGCCAGCCAAGCTGCTGTGAGACCAGCT	p.Ser33_Cys34insSerCysGlnProSerCysCysGluThrSer	conservative_inframe_insertion	1/1	6	NM_030966.2	ENSP00000344420.5		Q8IUG1

Frequencies

GnomAD3 genomes

AF:

0.0309

AC:

4381

AN:

141938

Hom.:

434

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0750

Gnomad AMI

AF:

0.0169

Gnomad AMR

AF:

0.0510

Gnomad ASJ

AF:

0.00919

Gnomad EAS

AF:

0.0868

Gnomad SAS

AF:

0.00897

Gnomad FIN

AF:

0.0116

Gnomad MID

AF:

0.0199

Gnomad NFE

AF:

0.00577

Gnomad OTH

AF:

0.0278

GnomAD3 exomes

AF:

0.0154

AC:

3602

AN:

234608

Hom.:

255

AF XY:

0.0132

AC XY:

1701

AN XY:

128560

show subpopulations

Gnomad AFR exome

AF:

0.0592

Gnomad AMR exome

AF:

0.0371

Gnomad ASJ exome

AF:

0.00389

Gnomad EAS exome

AF:

0.0786

Gnomad SAS exome

AF:

0.00535

Gnomad FIN exome

AF:

0.000680

Gnomad NFE exome

AF:

0.00226

Gnomad OTH exome

AF:

0.0148

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0109

AC:

15716

AN:

1442628

Hom.:

900

Cov.:

AF XY:

0.0109

AC XY:

7806

AN XY:

718156

show subpopulations

Gnomad4 AFR exome

AF:

0.0589

Gnomad4 AMR exome

AF:

0.0483

Gnomad4 ASJ exome

AF:

0.0129

Gnomad4 EAS exome

AF:

0.136

Gnomad4 SAS exome

AF:

0.00968

Gnomad4 FIN exome

AF:

0.0166

Gnomad4 NFE exome

AF:

0.00319

Gnomad4 OTH exome

AF:

0.0180

GnomAD4 genome

AF:

0.0309

AC:

4394

AN:

142046

Hom.:

435

Cov.:

AF XY:

0.0308

AC XY:

2133

AN XY:

69230

show subpopulations

Gnomad4 AFR

AF:

0.0752

Gnomad4 AMR

AF:

0.0509

Gnomad4 ASJ

AF:

0.00919

Gnomad4 EAS

AF:

0.0869

Gnomad4 SAS

AF:

0.00811

Gnomad4 FIN

AF:

0.0116

Gnomad4 NFE

AF:

0.00577

Gnomad4 OTH

AF:

0.0285

Alfa

AF:

0.00748

Hom.:

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Dec 31, 2019

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Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over