rs7910491

chr10-101093432-A-Gchr10-101093432-A-T

Variant summary

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

The NR_130723.1(TLX1NB):n.501-2730T>C 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 0.448 in 151,996 control chromosomes in the GnomAD database, including 15,357 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 0.45 (15357 hom., cov: 33)
• Consequence: TLX1NB NR_130723.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.18

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=-0.51).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TLX1NB	NR_130723.1	n.501-2730T>C		intron_variant, non_coding_transcript_variant
TLX1NB	NR_130722.1	n.530-2730T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TLX1NB	ENST00000445873.5	n.481-2730T>C		intron_variant, non_coding_transcript_variant		1
TLX1NB	ENST00000425505.1	n.510-2730T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.448 AC: 68073 AN: 151878 Hom.: 15352 Cov.: 33

Gnomad AFR AF: 0.467

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.372

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.462

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

GnomAD4 genome AF: 0.448 AC: 68107 AN: 151996 Hom.: 15357 Cov.: 33 AF XY: 0.448 AC XY: 33275 AN XY: 74296

Gnomad4 AFR AF: 0.467

Gnomad4 AMR AF: 0.426

Gnomad4 ASJ AF: 0.510

Gnomad4 EAS AF: 0.370

Gnomad4 SAS AF: 0.511

Gnomad4 FIN AF: 0.448

Gnomad4 NFE AF: 0.441

Gnomad4 OTH AF: 0.463

Alfa AF: 0.452 Hom.: 2492

Bravo AF: 0.445

Asia WGS AF: 0.495 AC: 1720 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
Cadd	Benign	13
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7910491; hg19: chr10-102853189;