17-41567173-CA-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_000226.4(KRT9):c.*40+59del variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.56 (22890 hom., cov: 0)
  • Exomes 𝑓: 0.44 (28061 hom.)
  • Failed GnomAD Quality Control
• Consequence: KRT9 NM_000226.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.05

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 17-41567173-CA-C is Benign according to our data. Variant chr17-41567173-CA-C is described in ClinVar as [Benign]. Clinvar id is 1286922.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.922 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KRT9	NM_000226.4	c.*40+59del		intron_variant		ENST00000246662.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KRT9	ENST00000246662.9	c.*40+59del		intron_variant		1	NM_000226.4	P1
KRT9	ENST00000588431.1	c.*40+59del		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.555 AC: 81150 AN: 146208 Hom.: 22878 Cov.: 0

Gnomad AFR AF: 0.470

Gnomad AMI AF: 0.691

Gnomad AMR AF: 0.652

Gnomad ASJ AF: 0.589

Gnomad EAS AF: 0.945

Gnomad SAS AF: 0.714

Gnomad FIN AF: 0.612

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.538

GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.440 AC: 551410 AN: 1254580 Hom.: 28061 AF XY: 0.440 AC XY: 274961 AN XY: 625042

Gnomad4 AFR exome AF: 0.405

Gnomad4 AMR exome AF: 0.510

Gnomad4 ASJ exome AF: 0.444

Gnomad4 EAS exome AF: 0.556

Gnomad4 SAS exome AF: 0.471

Gnomad4 FIN exome AF: 0.477

Gnomad4 NFE exome AF: 0.430

Gnomad4 OTH exome AF: 0.439

GnomAD4 genome AF: 0.555 AC: 81196 AN: 146282 Hom.: 22890 Cov.: 0 AF XY: 0.563 AC XY: 39981 AN XY: 70978

Gnomad4 AFR AF: 0.470

Gnomad4 AMR AF: 0.652

Gnomad4 ASJ AF: 0.589

Gnomad4 EAS AF: 0.945

Gnomad4 SAS AF: 0.714

Gnomad4 FIN AF: 0.612

Gnomad4 NFE AF: 0.533

Gnomad4 OTH AF: 0.539

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 12, 2021

- -

Computational scores

Source: dbNSFP v4.3

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: rs11313278; hg19: chr17-39723425;