10-101092859-G-A

Position:

• chr10-101092859-G-A

Variant summary

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

The NR_130723.1(TLX1NB):​n.501-2157C>T 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 0.913 in 152,298 control chromosomes in the GnomAD database, including 63,597 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 0.91 (63597 hom., cov: 34)
• Consequence: TLX1NB NR_130723.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.570

Genes affected

TLX1NB (HGNC:37183): (TLX1 neighbor)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TLX1NB	NR_130723.1	n.501-2157C>T		intron_variant, non_coding_transcript_variant
TLX1NB	NR_130722.1	n.530-2157C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TLX1NB	ENST00000445873.5	n.481-2157C>T		intron_variant, non_coding_transcript_variant		1
TLX1NB	ENST00000425505.1	n.510-2157C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.913 AC: 138936 AN: 152180 Hom.: 63529 Cov.: 34

Gnomad AFR AF: 0.969

Gnomad AMI AF: 0.792

Gnomad AMR AF: 0.892

Gnomad ASJ AF: 0.864

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.908

Gnomad FIN AF: 0.911

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.882

Gnomad OTH AF: 0.910

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

GnomAD4 genome AF: 0.913 AC: 139063 AN: 152298 Hom.: 63597 Cov.: 34 AF XY: 0.914 AC XY: 68092 AN XY: 74472

Gnomad4 AFR AF: 0.969

Gnomad4 AMR AF: 0.893

Gnomad4 ASJ AF: 0.864

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.909

Gnomad4 FIN AF: 0.911

Gnomad4 NFE AF: 0.882

Gnomad4 OTH AF: 0.911

Alfa AF: 0.899 Hom.: 7616

Bravo AF: 0.915

Asia WGS AF: 0.959 AC: 3336 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.39
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs807042; hg19: chr10-102852616;