NM_025159.3:c.858T>C

Variant names:

• chrX-30559498-A-G
• NM_025159.3:c.858T>C

Variant summary

Our verdict is Likely benign. The variant received -5 ACMG points: 2P and 7B. PM2 BP4_Strong BP6_Moderate BP7

The NM_025159.3(TASL):​c.858T>C​(p.Ile286Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000919 in 1,088,454 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: not found (cov: 23)
  • Exomes 𝑓: 9.2e-7 (0 hom. 0 hem.)
• Consequence: TASL NM_025159.3 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.240
• Publications: 0 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 -5 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BP6: Variant X-30559498-A-G is Benign according to our data. Variant chrX-30559498-A-G is described in ClinVar as Likely_benign. ClinVar VariationId is 2660234.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=0.24 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_025159.3. 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
	TASL	NM_025159.3	MANE Select	c.858T>C	p.Ile286Ile	synonymous	Exon 3 of 3	NP_079435.1	Q9HAI6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TASL	ENST00000378962.4	TSL:1 MANE Select	c.858T>C	p.Ile286Ile	synonymous	Exon 3 of 3	ENSP00000368245.3	Q9HAI6
	TASL	ENST00000955826.1		c.858T>C	p.Ile286Ile	synonymous	Exon 3 of 3	ENSP00000625885.1
	TASL	ENST00000955827.1		c.858T>C	p.Ile286Ile	synonymous	Exon 2 of 2	ENSP00000625886.1

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome AF: 9.19e-7 AC: 1 AN: 1088454 Hom.: 0 Cov.: 27 AF XY: 0.00 AC XY: 0 AN XY: 354530

African (AFR) AF: 0.00 AC: 0 AN: 26126

American (AMR) AF: 0.00 AC: 0 AN: 34489

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 18997

East Asian (EAS) AF: 0.00 AC: 0 AN: 30181

South Asian (SAS) AF: 0.00 AC: 0 AN: 52801

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 40374

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4087

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 835688

Other (OTH) AF: 0.0000219 AC: 1 AN: 45711

GnomAD4 genome Cov.: 23

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	7.5
DANN	Benign	0.72
PhyloP100		0.24

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

hg19: chrX-30577615;