18-36885549-T-TTTA

Position:

• chr18-36885549-T-TTTA

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP6

The NM_020776.3(KIAA1328):​c.333-8_333-7insTTA variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000478 in 1,296,686 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (no stars).

• Frequency:
  • Genomes: 𝑓 0.0 (0 hom., cov: 29)
  • Exomes 𝑓: 0.000048 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: KIAA1328 NM_020776.3 splice_region, splice_polypyrimidine_tract, intron
• Clinical Significance: Likely benign no assertion criteria provided B:1
• Conservation: PhyloP100: -0.964

Genes affected

KIAA1328 (HGNC:29248): (KIAA1328)

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP6: Variant 18-36885549-T-TTTA is Benign according to our data. Variant chr18-36885549-T-TTTA is described in ClinVar as [Likely_benign]. Clinvar id is 3032262.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIAA1328	NM_020776.3	c.333-8_333-7insTTA		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		ENST00000280020.10	NP_065827.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIAA1328	ENST00000280020.10	c.333-8_333-7insTTA		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		1	NM_020776.3	ENSP00000280020	P1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 151332 Hom.: 0 Cov.: 29 FAILED QC

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.0000702 AC: 9 AN: 128136 Hom.: 0 AF XY: 0.0000874 AC XY: 6 AN XY: 68624

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.000158

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.000129

Gnomad NFE exome AF: 0.0000853

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000478 AC: 62 AN: 1296686 Hom.: 0 Cov.: 21 AF XY: 0.0000451 AC XY: 29 AN XY: 643192

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.000220

Gnomad4 ASJ exome AF: 0.0000925

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000718

Gnomad4 FIN exome AF: 0.0000818

Gnomad4 NFE exome AF: 0.0000444

Gnomad4 OTH exome AF: 0.0000186

GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 151332 Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0 AN XY: 73860

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

Submissions by phenotype

KIAA1328-related disorder Benign:1

Likely benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Oct 07, 2022

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

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: rs1556808986; hg19: chr18-34465512;