rs9314704

chr9-81737032-G-Achr9-81737032-G-T

Variant summary

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

The NR_109772.1(TLE1-DT):n.248-10936G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.649 in 152,082 control chromosomes in the GnomAD database, including 32,824 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 0.65 (32824 hom., cov: 32)
• Consequence: TLE1-DT NR_109772.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.691

Genes affected

TLE1-DT (HGNC:55701): (TLE1 divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.787 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TLE1-DT	NR_109772.1	n.248-10936G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TLE1-DT	ENST00000437181.2	n.248-10936G>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.649 AC: 98661 AN: 151964 Hom.: 32772 Cov.: 32

Gnomad AFR AF: 0.794

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.650

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.596

Gnomad OTH AF: 0.644

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

GnomAD4 genome AF: 0.649 AC: 98770 AN: 152082 Hom.: 32824 Cov.: 32 AF XY: 0.647 AC XY: 48105 AN XY: 74322

Gnomad4 AFR AF: 0.794

Gnomad4 AMR AF: 0.607

Gnomad4 ASJ AF: 0.650

Gnomad4 EAS AF: 0.489

Gnomad4 SAS AF: 0.606

Gnomad4 FIN AF: 0.593

Gnomad4 NFE AF: 0.596

Gnomad4 OTH AF: 0.643

Alfa AF: 0.618 Hom.: 5917

Bravo AF: 0.657

Asia WGS AF: 0.557 AC: 1936 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.18
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9314704; hg19: chr9-84351947;