10-24958077-C-T

Position:

• chr10-24958077-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047425764.1(THNSL1):​c.-1697C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.427 in 151,928 control chromosomes in the GnomAD database, including 14,167 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 0.43 (14167 hom., cov: 33)
• Consequence: THNSL1 XM_047425764.1 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0540

Genes affected

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

ENSG00000285859 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.52 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
THNSL1	XM_047425764.1	c.-1697C>T		5_prime_UTR_premature_start_codon_gain_variant	1/4		XP_047281720.1
THNSL1	XM_047425764.1	c.-1697C>T		5_prime_UTR_variant	1/4		XP_047281720.1
THNSL1	XM_017016665.2	c.-285-3729C>T		intron_variant			XP_016872154.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000285859	ENST00000648191.1	n.100-3729C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.427 AC: 64833 AN: 151808 Hom.: 14159 Cov.: 33

Gnomad AFR AF: 0.527

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.398

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.416

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

GnomAD4 genome AF: 0.427 AC: 64870 AN: 151928 Hom.: 14167 Cov.: 33 AF XY: 0.424 AC XY: 31478 AN XY: 74216

Gnomad4 AFR AF: 0.526

Gnomad4 AMR AF: 0.397

Gnomad4 ASJ AF: 0.354

Gnomad4 EAS AF: 0.458

Gnomad4 SAS AF: 0.460

Gnomad4 FIN AF: 0.385

Gnomad4 NFE AF: 0.380

Gnomad4 OTH AF: 0.413

Alfa AF: 0.380 Hom.: 16389

Bravo AF: 0.437

Asia WGS AF: 0.413 AC: 1435 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.6
DANN	Benign	0.46

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs274304; hg19: chr10-25247006;