rs1008307577

Variant names:

• chr10-25023330-C-A
• rs1008307577
• NM_024838.5:c.107C>A

Your query was ambiguous. Multiple possible variants found:

• chr10-25023330-C-A
• chr10-25023330-C-T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_024838.5(THNSL1):​c.107C>A​(p.Thr36Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T36I) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: THNSL1 NM_024838.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.18
• Publications: 0 publications found

Genes affected

THNSL1 (HGNC:26160): (threonine synthase like 1)

ENKUR (HGNC:28388): (enkurin, TRPC channel interacting protein) This gene encodes a protein that interacts with calmodulin and several transient receptor potential canonical cation channel proteins. The encoded protein may function as an adaptor to localize signal transduction machinery to calcium channels. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2012]

ENSG00000285859 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.09847048).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
THNSL1	NM_024838.5	c.107C>A	p.Thr36Asn	missense_variant	Exon 3 of 3	ENST00000376356.5	NP_079114.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
THNSL1	ENST00000376356.5	c.107C>A	p.Thr36Asn	missense_variant	Exon 3 of 3	1	NM_024838.5	ENSP00000365534.4
ENKUR	ENST00000615958.4	c.38-27461G>T		intron_variant	Intron 2 of 5	1		ENSP00000478989.1
THNSL1	ENST00000524413.5	c.107C>A	p.Thr36Asn	missense_variant	Exon 3 of 3	3		ENSP00000434887.1
ENSG00000285859	ENST00000648191.1	n.336+1422C>A		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.076
BayesDel_addAF	Benign	-0.29	T
BayesDel_noAF	Benign	-0.66
CADD	Benign	15
DANN	Benign	0.95
DEOGEN2	Benign	0.0016	T;T
Eigen	Benign	-0.22
Eigen_PC	Benign	-0.055
FATHMM_MKL	Benign	0.37	N
LIST_S2	Benign	0.62	.;T
M_CAP	Benign	0.0045	T
MetaRNN	Benign	0.098	T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	1.7	L;L
PhyloP100		1.2
PrimateAI	Benign	0.29	T
PROVEAN	Benign	-0.57	N;N
REVEL	Benign	0.072
Sift	Uncertain	0.022	D;D
Sift4G	Benign	0.33	T;T
Polyphen		0.047	B;B
Vest4		0.14
MutPred		0.38		Gain of MoRF binding (P = 0.1348);Gain of MoRF binding (P = 0.1348);
MVP		0.24
MPC		0.036
ClinPred		0.10	T
GERP RS		5.0
Varity_R		0.11
gMVP		0.29
Mutation Taster		=87/13	polymorphism

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: rs1008307577; hg19: chr10-25312259;