rs1544545

chrX-30568646-T-AchrX-30568646-T-CchrX-30568646-T-G

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

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

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

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BS2: High Homozygotes in GnomAd at 21085 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TASL	NM_025159.3	c.-2+8106A>T		intron_variant		ENST00000378962.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TASL	ENST00000378962.4	c.-2+8106A>T		intron_variant		1	NM_025159.3	P1

Frequencies

GnomAD3 genomes AF: 0.731 AC: 79756 AN: 109081 Hom.: 21085 Cov.: 21 AF XY: 0.735 AC XY: 23071 AN XY: 31371

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

Gnomad4 AFR AF: 0.831

Gnomad4 AMR AF: 0.792

Gnomad4 ASJ AF: 0.527

Gnomad4 EAS AF: 0.939

Gnomad4 SAS AF: 0.875

Gnomad4 FIN AF: 0.746

Gnomad4 NFE AF: 0.653

Gnomad4 OTH AF: 0.691

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

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: rs1544545; hg19: chrX-30586763;