11-1629968-G-GGGGCTGTGGCTC

Position:

• chr11-1629968-G-GGGGCTGTGGCTC

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM4 BP6_Moderate BS2

The NM_001001480.3(KRTAP5-5):​c.128_129insGGGCTGTGGCTC​(p.Gly43_Gly44insGlyCysGlySer) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0024 (6 hom., cov: 11)
  • Exomes 𝑓: 0.0020 (11 hom.)
  • Failed GnomAD Quality Control
• Consequence: KRTAP5-5 NM_001001480.3 disruptive_inframe_insertion
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -6.10

Genes affected

KRTAP5-5 (HGNC:23601): (keratin associated protein 5-5) Predicted to act upstream of or within hematopoietic progenitor cell differentiation. Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• PM4: Nonframeshift variant in NON repetitive region in NM_001001480.3.
• BP6: Variant 11-1629968-G-GGGGCTGTGGCTC is Benign according to our data. Variant chr11-1629968-G-GGGGCTGTGGCTC is described in ClinVar as [Likely_benign]. Clinvar id is 2641349.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAd4 at 6 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KRTAP5-5	NM_001001480.3	c.128_129insGGGCTGTGGCTC	p.Gly43_Gly44insGlyCysGlySer	disruptive_inframe_insertion	1/1	ENST00000399676.4	NP_001001480.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KRTAP5-5	ENST00000399676.4	c.128_129insGGGCTGTGGCTC	p.Gly43_Gly44insGlyCysGlySer	disruptive_inframe_insertion	1/1	6	NM_001001480.3	ENSP00000382584.2

Frequencies

GnomAD3 genomes AF: 0.00240 AC: 248 AN: 103120 Hom.: 6 Cov.: 11

Gnomad AFR AF: 0.00237

Gnomad AMI AF: 0.00162

Gnomad AMR AF: 0.00171

Gnomad ASJ AF: 0.000725

Gnomad EAS AF: 0.00111

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000323

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00327

Gnomad OTH AF: 0.00143

GnomAD3 exomes AF: 0.00158 AC: 257 AN: 162300 Hom.: 2 AF XY: 0.00148 AC XY: 131 AN XY: 88552

Gnomad AFR exome AF: 0.0119

Gnomad AMR exome AF: 0.000670

Gnomad ASJ exome AF: 0.000143

Gnomad EAS exome AF: 0.000317

Gnomad SAS exome AF: 0.000426

Gnomad FIN exome AF: 0.000443

Gnomad NFE exome AF: 0.00157

Gnomad OTH exome AF: 0.00261

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00200 AC: 1996 AN: 997858 Hom.: 11 Cov.: 47 AF XY: 0.00199 AC XY: 994 AN XY: 498636

Gnomad4 AFR exome AF: 0.00554

Gnomad4 AMR exome AF: 0.00137

Gnomad4 ASJ exome AF: 0.00103

Gnomad4 EAS exome AF: 0.000498

Gnomad4 SAS exome AF: 0.000735

Gnomad4 FIN exome AF: 0.00170

Gnomad4 NFE exome AF: 0.00211

Gnomad4 OTH exome AF: 0.00250

GnomAD4 genome AF: 0.00240 AC: 248 AN: 103200 Hom.: 6 Cov.: 11 AF XY: 0.00226 AC XY: 112 AN XY: 49538

Gnomad4 AFR AF: 0.00236

Gnomad4 AMR AF: 0.00170

Gnomad4 ASJ AF: 0.000725

Gnomad4 EAS AF: 0.00111

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000323

Gnomad4 NFE AF: 0.00328

Gnomad4 OTH AF: 0.00142

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

Jan 01, 2023

KRTAP5-5: 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: rs778993095; hg19: chr11-1651198;