9-85402691-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000669133.1(ENSG00000285634):n.142-4G>A variant causes a splice region, splice polypyrimidine tract, intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0958 in 152,108 control chromosomes in the GnomAD database, including 2,009 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.096 (2009 hom., cov: 33)
• Consequence: ENST00000669133.1 splice_region, splice_polypyrimidine_tract, intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.420

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.698 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376121	XR_001746810.2	n.312-4G>A		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000669133.1	n.142-4G>A		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0959 AC: 14571 AN: 151990 Hom.: 2011 Cov.: 33

Gnomad AFR AF: 0.0783

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.0762

Gnomad ASJ AF: 0.0589

Gnomad EAS AF: 0.717

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0450

Gnomad OTH AF: 0.0800

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0958 AC: 14572 AN: 152108 Hom.: 2009 Cov.: 33 AF XY: 0.108 AC XY: 8003 AN XY: 74382

Gnomad4 AFR AF: 0.0784

Gnomad4 AMR AF: 0.0761

Gnomad4 ASJ AF: 0.0589

Gnomad4 EAS AF: 0.717

Gnomad4 SAS AF: 0.307

Gnomad4 FIN AF: 0.140

Gnomad4 NFE AF: 0.0449

Gnomad4 OTH AF: 0.0801

Alfa AF: 0.0574 Hom.: 1384

Bravo AF: 0.0912

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	5.6
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12685505; hg19: chr9-88017606;