10-24958077-C-T

Variant names:

• chr10-24958077-C-T
• rs274304
• XM_047425764.1:c.-1697C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

Genes affected

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

ENSG00000285859 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648191.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285859	ENST00000648191.1		n.100-3729C>T		intron	N/A

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

African (AFR) AF: 0.526 AC: 21800 AN: 41440

American (AMR) AF: 0.397 AC: 6057 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.354 AC: 1230 AN: 3470

East Asian (EAS) AF: 0.458 AC: 2372 AN: 5176

South Asian (SAS) AF: 0.460 AC: 2209 AN: 4806

European-Finnish (FIN) AF: 0.385 AC: 4033 AN: 10486

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.380 AC: 25848 AN: 67966

Other (OTH) AF: 0.413 AC: 869 AN: 2104

Alfa AF: 0.384 Hom.: 22500

Bravo AF: 0.437

Asia WGS AF: 0.413 AC: 1435 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.6
DANN	Benign	0.46
PhyloP100		0.054

Splicing

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

Other links and lift over

dbSNP: rs274304; hg19: chr10-25247006;