9-69385787-TAA-T

Position:

• chr9-69385787-TAA-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_001347995.2(ENTREP1):​c.1163-6_1163-5delAA variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000243 in 946,212 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00035 (0 hom., cov: 0)
  • Exomes 𝑓: 0.000024 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENTREP1 NM_001347995.2 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.410

Genes affected

ENTREP1 (HGNC:24820): (endosomal transmembrane epsin interactor 1) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ENTREP1 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ENTREP1	NM_001347995.2	c.1163-6_1163-5delAA		splice_region_variant, intron_variant		ENST00000303068.14	NP_001334924.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENTREP1	ENST00000303068.14	c.1163-6_1163-5delAA		splice_region_variant, intron_variant		2	NM_001347995.2	ENSP00000304435.8

Frequencies

GnomAD3 genomes AF: 0.00 AC: 18 AN: 51900 Hom.: 0 Cov.: 0 FAILED QC

Gnomad AFR AF: 0.000342

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000766

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: 0.000388

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0000243 AC: 23 AN: 946212 Hom.: 0 AF XY: 0.0000287 AC XY: 13 AN XY: 453206

Gnomad4 AFR exome AF: 0.0000582

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.000178

Gnomad4 EAS exome AF: 0.0000587

Gnomad4 SAS exome AF: 0.0000803

Gnomad4 FIN exome AF: 0.0000399

Gnomad4 NFE exome AF: 0.0000164

Gnomad4 OTH exome AF: 0.0000570

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.000347 AC: 18 AN: 51930 Hom.: 0 Cov.: 0 AF XY: 0.000322 AC XY: 8 AN XY: 24862

Gnomad4 AFR AF: 0.000341

Gnomad4 AMR AF: 0.000764

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000388

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs193921010; hg19: chr9-72000703;