11-1585151-AGAGCCACAGCCCCCACAGCCG-A

Position:

• chr11-1585151-AGAGCCACAGCCCCCACAGCCG-A

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP3 BP6_Moderate BS2

The NM_001005922.1(KRTAP5-1):​c.78_98del​(p.Cys31_Gly37del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00783 in 136,670 control chromosomes in the GnomAD database, including 5 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0078 (5 hom., cov: 29)
  • Exomes 𝑓: 0.0052 (69 hom.)
  • Failed GnomAD Quality Control
• Consequence: KRTAP5-1 NM_001005922.1 inframe_deletion
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 2.12

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:27877): (KRTAP5-1/KRTAP5-2 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -7 ACMG points.

• BP3: Nonframeshift variant in repetitive region in NM_001005922.1
• BP6: Variant 11-1585151-AGAGCCACAGCCCCCACAGCCG-A is Benign according to our data. Variant chr11-1585151-AGAGCCACAGCCCCCACAGCCG-A is described in ClinVar as [Likely_benign]. Clinvar id is 2641347.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAd4 at 5 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KRTAP5-1	NM_001005922.1	c.78_98del	p.Cys31_Gly37del	inframe_deletion	1/1	ENST00000382171.2	NP_001005922.1
KRTAP5-AS1	NR_021489.2	n.329-12056_329-12036del		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KRTAP5-1	ENST00000382171.2	c.78_98del	p.Cys31_Gly37del	inframe_deletion	1/1		NM_001005922.1	ENSP00000371606	P1
KRTAP5-AS1	ENST00000424148.1	n.329-12056_329-12036del		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.00781 AC: 1066 AN: 136530 Hom.: 4 Cov.: 29

Gnomad AFR AF: 0.00967

Gnomad AMI AF: 0.00121

Gnomad AMR AF: 0.00783

Gnomad ASJ AF: 0.00759

Gnomad EAS AF: 0.000943

Gnomad SAS AF: 0.00299

Gnomad FIN AF: 0.000886

Gnomad MID AF: 0.0123

Gnomad NFE AF: 0.00848

Gnomad OTH AF: 0.0109

GnomAD3 exomes AF: 0.00505 AC: 1256 AN: 248844 Hom.: 4 AF XY: 0.00504 AC XY: 679 AN XY: 134768

Gnomad AFR exome AF: 0.00841

Gnomad AMR exome AF: 0.00549

Gnomad ASJ exome AF: 0.00710

Gnomad EAS exome AF: 0.000437

Gnomad SAS exome AF: 0.00162

Gnomad FIN exome AF: 0.000696

Gnomad NFE exome AF: 0.00671

Gnomad OTH exome AF: 0.00593

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00520 AC: 7394 AN: 1421484 Hom.: 69 AF XY: 0.00534 AC XY: 3779 AN XY: 707268

Gnomad4 AFR exome AF: 0.00732

Gnomad4 AMR exome AF: 0.00551

Gnomad4 ASJ exome AF: 0.00759

Gnomad4 EAS exome AF: 0.000321

Gnomad4 SAS exome AF: 0.00183

Gnomad4 FIN exome AF: 0.000974

Gnomad4 NFE exome AF: 0.00567

Gnomad4 OTH exome AF: 0.00606

GnomAD4 genome AF: 0.00783 AC: 1070 AN: 136670 Hom.: 5 Cov.: 29 AF XY: 0.00753 AC XY: 501 AN XY: 66508

Gnomad4 AFR AF: 0.00976

Gnomad4 AMR AF: 0.00782

Gnomad4 ASJ AF: 0.00759

Gnomad4 EAS AF: 0.000944

Gnomad4 SAS AF: 0.00299

Gnomad4 FIN AF: 0.000886

Gnomad4 NFE AF: 0.00848

Gnomad4 OTH AF: 0.0107

Asia WGS AF: 0.00144 AC: 5 AN: 3478

EpiCase AF: 0.00939

EpiControl AF: 0.00672

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

Feb 01, 2023

KRTAP5-1: BS2 -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs754294371; hg19: chr11-1606381;