Variant 17-41567173-C-CA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_000226.4(KRT9):c.*40+59_*40+60insT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 1,385,652 control chromosomes in the GnomAD database, including 826 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.090 ( 615 hom., cov: 0)

Exomes 𝑓: 0.12 ( 211 hom. )

Consequence

KRT9
NM_000226.4 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.05

Variant links:

Genes affected

KRT9 (HGNC:6447): (keratin 9) This gene encodes the type I keratin 9, an intermediate filament chain expressed only in the terminally differentiated epidermis of palms and soles. Mutations in this gene cause epidermolytic palmoplantar keratoderma. [provided by RefSeq, Jul 2008]

KRT9 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 17-41567173-C-CA is Benign according to our data. Variant chr17-41567173-C-CA is described in ClinVar as [Benign]. Clinvar id is 1232956.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.112 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KRT9	NM_000226.4 linkuse as main transcript	c.40+59_40+60insT		intron_variant		ENST00000246662.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KRT9	ENST00000246662.9 linkuse as main transcript	c.40+59_40+60insT		intron_variant		1	NM_000226.4	P1
KRT9	ENST00000588431.1 linkuse as main transcript	c.40+59_40+60insT		intron_variant		1

Frequencies

GnomAD3 genomes

AF:

0.0904

AC:

13217

AN:

146272

Hom.:

620

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0701

Gnomad AMI

AF:

0.0325

Gnomad AMR

AF:

0.0711

Gnomad ASJ

AF:

0.114

Gnomad EAS

AF:

0.0509

Gnomad SAS

AF:

0.120

Gnomad FIN

AF:

0.0673

Gnomad MID

AF:

0.192

Gnomad NFE

AF:

0.109

Gnomad OTH

AF:

0.113

GnomAD4 exome

AF:

0.120

AC:

148585

AN:

1239304

Hom.:

211

AF XY:

0.120

AC XY:

74358

AN XY:

617478

show subpopulations

Gnomad4 AFR exome

AF:

0.0944

Gnomad4 AMR exome

AF:

0.0613

Gnomad4 ASJ exome

AF:

0.124

Gnomad4 EAS exome

AF:

0.0456

Gnomad4 SAS exome

AF:

0.122

Gnomad4 FIN exome

AF:

0.0725

Gnomad4 NFE exome

AF:

0.127

Gnomad4 OTH exome

AF:

0.120

GnomAD4 genome

AF:

0.0903

AC:

13215

AN:

146348

Hom.:

615

Cov.:

AF XY:

0.0892

AC XY:

6336

AN XY:

71004

show subpopulations

Gnomad4 AFR

AF:

0.0701

Gnomad4 AMR

AF:

0.0710

Gnomad4 ASJ

AF:

0.114

Gnomad4 EAS

AF:

0.0506

Gnomad4 SAS

AF:

0.120

Gnomad4 FIN

AF:

0.0673

Gnomad4 NFE

AF:

0.109

Gnomad4 OTH

AF:

0.112

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

GeneDx

May 12, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

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