rs1111350

Positions:

• chr10-101130664-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.361+122C>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 0.164 in 180,148 control chromosomes in the GnomAD database, including 2,602 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 (2061 hom., cov: 32)
  • Exomes 𝑓: 0.19 (541 hom.)
• Consequence: TLX1NB NR_130723.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.954

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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.24 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TLX1NB	NR_130723.1	n.361+122C>T		intron_variant, non_coding_transcript_variant
TLX1NB	NR_130722.1	n.390+93C>T		intron_variant, non_coding_transcript_variant
TLX1NB	NR_130724.1	n.580-3566C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TLX1NB	ENST00000445873.5	n.341+122C>T		intron_variant, non_coding_transcript_variant		1
TLX1NB	ENST00000425505.1	n.370+93C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24191 AN: 152050 Hom.: 2057 Cov.: 32

Gnomad AFR AF: 0.0940

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.252

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.152

GnomAD4 exome AF: 0.188 AC: 5261 AN: 27980 Hom.: 541 Cov.: 0 AF XY: 0.190 AC XY: 2423 AN XY: 12762

Gnomad4 AFR exome AF: 0.123

Gnomad4 AMR exome AF: 0.205

Gnomad4 ASJ exome AF: 0.148

Gnomad4 EAS exome AF: 0.286

Gnomad4 SAS exome AF: 0.199

Gnomad4 FIN exome AF: 0.278

Gnomad4 NFE exome AF: 0.164

Gnomad4 OTH exome AF: 0.171

GnomAD4 genome AF: 0.159 AC: 24209 AN: 152168 Hom.: 2061 Cov.: 32 AF XY: 0.165 AC XY: 12244 AN XY: 74386

Gnomad4 AFR AF: 0.0939

Gnomad4 AMR AF: 0.194

Gnomad4 ASJ AF: 0.164

Gnomad4 EAS AF: 0.252

Gnomad4 SAS AF: 0.187

Gnomad4 FIN AF: 0.244

Gnomad4 NFE AF: 0.169

Gnomad4 OTH AF: 0.152

Alfa AF: 0.167 Hom.: 2587

Bravo AF: 0.155

Asia WGS AF: 0.177 AC: 613 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.4
DANN	Benign	0.49

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1111350; hg19: chr10-102890421;