10-24822981-T-G

Position:

• chr10-24822981-T-G

Variant summary

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

The 10-24822981-T-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: ENST00000649039.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000649039.1			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;