rs1556864

Positions:

• chr10-101118852-T-A

Variant summary

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

The NR_130723.1(TLX1NB):​n.500+8108A>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 0.159 in 152,262 control chromosomes in the GnomAD database, including 2,325 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 0.16 (2325 hom., cov: 32)
• Consequence: TLX1NB NR_130723.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.25

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=-0.49).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.212 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TLX1NB	NR_130723.1	n.500+8108A>T		intron_variant, non_coding_transcript_variant
TLX1NB	NR_130722.1	n.529+8108A>T		intron_variant, non_coding_transcript_variant
TLX1NB	NR_130724.1	n.719-3612A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TLX1NB	ENST00000445873.5	n.480+8108A>T		intron_variant, non_coding_transcript_variant		1
TLX1NB	ENST00000425505.1	n.509+8108A>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24166 AN: 152144 Hom.: 2319 Cov.: 32

Gnomad AFR AF: 0.0549

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.0673

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.159 AC: 24186 AN: 152262 Hom.: 2325 Cov.: 32 AF XY: 0.157 AC XY: 11652 AN XY: 74448

Gnomad4 AFR AF: 0.0550

Gnomad4 AMR AF: 0.181

Gnomad4 ASJ AF: 0.166

Gnomad4 EAS AF: 0.193

Gnomad4 SAS AF: 0.0676

Gnomad4 FIN AF: 0.193

Gnomad4 NFE AF: 0.215

Gnomad4 OTH AF: 0.164

Alfa AF: 0.180 Hom.: 346

Bravo AF: 0.153

Asia WGS AF: 0.105 AC: 368 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	14
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1556864; hg19: chr10-102878609;