12-75506616-C-CAAAAAAAAAAA

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6_Moderate

The NM_007043.7(KRR1):c.394-8_394-7insTTTTTTTTTTT variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0061 (3 hom., cov: 0)
  • Exomes 𝑓: 0.0013 (42 hom.)
  • Failed GnomAD Quality Control
• Consequence: KRR1 NM_007043.7 splice_region, splice_polypyrimidine_tract, intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0340

Genes affected

KRR1 (HGNC:5176): (KRR1 small subunit processome component homolog) Enables RNA binding activity. Predicted to be involved in rRNA processing. Located in chromosome; intercellular bridge; and nuclear lumen. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• BP6: Variant 12-75506616-C-CAAAAAAAAAAA is Benign according to our data. Variant chr12-75506616-C-CAAAAAAAAAAA is described in ClinVar as [Likely_benign]. Clinvar id is 2643183.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KRR1	NM_007043.7	c.394-8_394-7insTTTTTTTTTTT		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		ENST00000229214.9
KRR1	XM_047428133.1	c.100-8_100-7insTTTTTTTTTTT		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KRR1	ENST00000229214.9	c.394-8_394-7insTTTTTTTTTTT		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		1	NM_007043.7	P1
KRR1	ENST00000438169.6	c.394-8_394-7insTTTTTTTTTTT		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		1
KRR1	ENST00000550898.1	n.597_598insTTTTTTTTTTT		non_coding_transcript_exon_variant	3/3	2
KRR1	ENST00000550023.5	n.410-8_410-7insTTTTTTTTTTT		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.00 AC: 745 AN: 122794 Hom.: 3 Cov.: 0 FAILED QC

Gnomad AFR AF: 0.00465

Gnomad AMI AF: 0.00837

Gnomad AMR AF: 0.00430

Gnomad ASJ AF: 0.00635

Gnomad EAS AF: 0.00226

Gnomad SAS AF: 0.00428

Gnomad FIN AF: 0.000896

Gnomad MID AF: 0.00435

Gnomad NFE AF: 0.00799

Gnomad OTH AF: 0.00616

GnomAD4 exome AF: 0.00127 AC: 1582 AN: 1248436 Hom.: 42 Cov.: 0 AF XY: 0.00152 AC XY: 930 AN XY: 613092

Gnomad4 AFR exome AF: 0.00339

Gnomad4 AMR exome AF: 0.00389

Gnomad4 ASJ exome AF: 0.00171

Gnomad4 EAS exome AF: 0.00115

Gnomad4 SAS exome AF: 0.00641

Gnomad4 FIN exome AF: 0.00129

Gnomad4 NFE exome AF: 0.000835

Gnomad4 OTH exome AF: 0.00117

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00608 AC: 746 AN: 122772 Hom.: 3 Cov.: 0 AF XY: 0.00561 AC XY: 328 AN XY: 58462

Gnomad4 AFR AF: 0.00468

Gnomad4 AMR AF: 0.00429

Gnomad4 ASJ AF: 0.00635

Gnomad4 EAS AF: 0.00227

Gnomad4 SAS AF: 0.00430

Gnomad4 FIN AF: 0.000896

Gnomad4 NFE AF: 0.00800

Gnomad4 OTH AF: 0.00613

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

KRR1: BP4, 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: rs35071517; hg19: chr12-75900396;