chr5-160412523-T-TAAAAAAAAA

Position:

• chr5-160412523-T-TAAAAAAAAA

Variant summary

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

The NM_006425.5(SLU7):​c.571-13_571-5dupTTTTTTTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0014 (0 hom., cov: 0)
  • Exomes 𝑓: 0.0013 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SLU7 NM_006425.5 splice_region, intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0460

Genes affected

SLU7 (HGNC:16939): (SLU7 homolog, splicing factor) Pre-mRNA splicing occurs in two sequential transesterification steps. The protein encoded by this gene is a splicing factor that has been found to be essential during the second catalytic step in the pre-mRNA splicing process. It associates with the spliceosome and contains a zinc knuckle motif that is found in other splicing factors and is involved in protein-nucleic acid and protein-protein interactions. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• BP6: Variant 5-160412523-T-TAAAAAAAAA is Benign according to our data. Variant chr5-160412523-T-TAAAAAAAAA is described in ClinVar as [Likely_benign]. Clinvar id is 2861674.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLU7	NM_006425.5	c.571-13_571-5dupTTTTTTTTT		splice_region_variant, intron_variant		ENST00000297151.9	NP_006416.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLU7	ENST00000297151.9	c.571-13_571-5dupTTTTTTTTT		splice_region_variant, intron_variant		1	NM_006425.5	ENSP00000297151.4

Frequencies

GnomAD3 genomes AF: 0.00139 AC: 134 AN: 96262 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000565

Gnomad AMI AF: 0.00685

Gnomad AMR AF: 0.00125

Gnomad ASJ AF: 0.00122

Gnomad EAS AF: 0.00196

Gnomad SAS AF: 0.000752

Gnomad FIN AF: 0.000292

Gnomad MID AF: 0.00521

Gnomad NFE AF: 0.00192

Gnomad OTH AF: 0.00162

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00133 AC: 981 AN: 739354 Hom.: 0 Cov.: 18 AF XY: 0.00133 AC XY: 504 AN XY: 377996

Gnomad4 AFR exome AF: 0.00214

Gnomad4 AMR exome AF: 0.00167

Gnomad4 ASJ exome AF: 0.00168

Gnomad4 EAS exome AF: 0.000722

Gnomad4 SAS exome AF: 0.00270

Gnomad4 FIN exome AF: 0.00103

Gnomad4 NFE exome AF: 0.00122

Gnomad4 OTH exome AF: 0.00169

GnomAD4 genome AF: 0.00139 AC: 134 AN: 96276 Hom.: 0 Cov.: 0 AF XY: 0.00152 AC XY: 68 AN XY: 44740

Gnomad4 AFR AF: 0.000565

Gnomad4 AMR AF: 0.00125

Gnomad4 ASJ AF: 0.00122

Gnomad4 EAS AF: 0.00197

Gnomad4 SAS AF: 0.000756

Gnomad4 FIN AF: 0.000292

Gnomad4 NFE AF: 0.00192

Gnomad4 OTH AF: 0.00161

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

Labcorp Genetics (formerly Invitae), Labcorp

Jan 12, 2024

- -

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: rs57812151; hg19: chr5-159839530;