rs1556864

Variant names:

• chr10-101118852-T-A
• rs1556864
• ENST00000445873.5:n.480+8108A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000445873.5(TLX1NB):​n.480+8108A>T variant causes a intron 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 ENST00000445873.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.25
• Publications: 2 publications found

Genes affected

TLX1NB (HGNC:37183): (TLX1 neighbor)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000445873.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TLX1NB	NR_130722.1		n.529+8108A>T		intron	N/A
	TLX1NB	NR_130723.1		n.500+8108A>T		intron	N/A
	TLX1NB	NR_130724.1		n.719-3612A>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TLX1NB	ENST00000445873.5	TSL:1	n.480+8108A>T		intron	N/A
	TLX1NB	ENST00000425505.2	TSL:3	n.544+8108A>T		intron	N/A
	TLX1NB	ENST00000747503.1		n.870+8108A>T		intron	N/A

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

African (AFR) AF: 0.0550 AC: 2286 AN: 41566

American (AMR) AF: 0.181 AC: 2774 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 577 AN: 3472

East Asian (EAS) AF: 0.193 AC: 1000 AN: 5188

South Asian (SAS) AF: 0.0676 AC: 326 AN: 4826

European-Finnish (FIN) AF: 0.193 AC: 2046 AN: 10594

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.215 AC: 14605 AN: 68010

Other (OTH) AF: 0.164 AC: 347 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	14
DANN	Benign	0.83
PhyloP100		1.2
Mutation Taster		=96/4	polymorphism (auto)

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1556864;

hg19: chr10-102878609;