rs7910491

Variant names:

• chr10-101093432-A-G
• rs7910491
• ENST00000445873.5:n.481-2730T>C

Your query was ambiguous. Multiple possible variants found:

• chr10-101093432-A-G
• chr10-101093432-A-T

Variant summary

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

The ENST00000445873.5(TLX1NB):​n.481-2730T>C variant causes a intron 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 ENST00000445873.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.18
• Publications: 3 publications found

Genes affected

TLX1NB (HGNC:37183): (TLX1 neighbor)

ENSG00000297415 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

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.530-2730T>C		intron	N/A
	TLX1NB	NR_130723.1		n.501-2730T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TLX1NB	ENST00000445873.5	TSL:1	n.481-2730T>C		intron	N/A
	TLX1NB	ENST00000425505.2	TSL:3	n.545-2730T>C		intron	N/A
	TLX1NB	ENST00000747503.1		n.871-2730T>C		intron	N/A

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

African (AFR) AF: 0.467 AC: 19357 AN: 41462

American (AMR) AF: 0.426 AC: 6516 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.510 AC: 1769 AN: 3468

East Asian (EAS) AF: 0.370 AC: 1913 AN: 5164

South Asian (SAS) AF: 0.511 AC: 2465 AN: 4828

European-Finnish (FIN) AF: 0.448 AC: 4743 AN: 10576

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.441 AC: 29930 AN: 67906

Other (OTH) AF: 0.463 AC: 977 AN: 2110

Alfa AF: 0.453 Hom.: 2577

Bravo AF: 0.445

Asia WGS AF: 0.495 AC: 1720 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	13
DANN	Benign	0.70
PhyloP100		1.2
Mutation Taster		=100/0	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: rs7910491;

hg19: chr10-102853189;