10-24822981-T-G

Variant names:

• chr10-24822981-T-G
• rs11014249
• ENST00000649039.1:n.*31T>G

Variant summary

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

The ENST00000649039.1(ENSG00000285750):​n.*31T>G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.355 in 152,102 control chromosomes in the GnomAD database, including 10,003 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 0.35 (10003 hom., cov: 33)
• Consequence: ENSG00000285750 ENST00000649039.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308

Genes affected

ENSG00000285750 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285750	ENST00000649039.1	n.*31T>G		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.355 AC: 53937 AN: 151984 Hom.: 9995 Cov.: 33

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.505

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.355 AC: 53976 AN: 152102 Hom.: 10003 Cov.: 33 AF XY: 0.355 AC XY: 26381 AN XY: 74352

Gnomad4 AFR AF: 0.314

Gnomad4 AMR AF: 0.283

Gnomad4 ASJ AF: 0.284

Gnomad4 EAS AF: 0.168

Gnomad4 SAS AF: 0.295

Gnomad4 FIN AF: 0.505

Gnomad4 NFE AF: 0.397

Gnomad4 OTH AF: 0.299

Alfa AF: 0.323 Hom.: 1541

Asia WGS AF: 0.237 AC: 824 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	7.7
DANN	Benign	0.91

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11014249; hg19: chr10-25111910;