rs1544545

Variant names:

• chrX-30568646-T-A
• rs1544545
• NM_025159.3:c.-2+8106A>T

Your query was ambiguous. Multiple possible variants found:

• chrX-30568646-T-A
• chrX-30568646-T-C
• chrX-30568646-T-G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_025159.3(TASL):​c.-2+8106A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.73 (21078 hom., 23127 hem., cov: 21)
  • Failed GnomAD Quality Control
• Consequence: TASL NM_025159.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.566
• Publications: 2 publications found

Genes affected

TASL (HGNC:25667): (TLR adaptor interacting with endolysosomal SLC15A4) Involved in positive regulation of innate immune response; positive regulation of toll-like receptor signaling pathway; and regulation of lysosomal lumen pH. Located in endolysosome membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TASL	NM_025159.3	c.-2+8106A>T		intron_variant	Intron 2 of 2	ENST00000378962.4	NP_079435.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TASL	ENST00000378962.4	c.-2+8106A>T		intron_variant	Intron 2 of 2	1	NM_025159.3	ENSP00000368245.3

Frequencies

GnomAD3 genomes AF: 0.731 AC: 79756 AN: 109081 Hom.: 21085 Cov.: 21

Gnomad AFR AF: 0.831

Gnomad AMI AF: 0.681

Gnomad AMR AF: 0.792

Gnomad ASJ AF: 0.527

Gnomad EAS AF: 0.939

Gnomad SAS AF: 0.876

Gnomad FIN AF: 0.746

Gnomad MID AF: 0.588

Gnomad NFE AF: 0.653

Gnomad OTH AF: 0.696

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.731 AC: 79800 AN: 109133 Hom.: 21078 Cov.: 21 AF XY: 0.736 AC XY: 23127 AN XY: 31433

African (AFR) AF: 0.831 AC: 24906 AN: 29959

American (AMR) AF: 0.792 AC: 8093 AN: 10218

Ashkenazi Jewish (ASJ) AF: 0.527 AC: 1379 AN: 2616

East Asian (EAS) AF: 0.939 AC: 3263 AN: 3476

South Asian (SAS) AF: 0.875 AC: 2188 AN: 2502

European-Finnish (FIN) AF: 0.746 AC: 4158 AN: 5577

Middle Eastern (MID) AF: 0.599 AC: 127 AN: 212

European-Non Finnish (NFE) AF: 0.653 AC: 34218 AN: 52439

Other (OTH) AF: 0.691 AC: 1014 AN: 1467

Alfa AF: 0.698 Hom.: 5619

Bravo AF: 0.743

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.6
DANN	Benign	0.77
PhyloP100		0.57
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1544545; hg19: chrX-30586763;