chr10-24822981-T-G

Variant names:

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

Variant summary

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

Genes affected

ENSG00000285750 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000649039.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285750	ENST00000649039.1		n.*31T>G		downstream_gene	N/A

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

African (AFR) AF: 0.314 AC: 13038 AN: 41468

American (AMR) AF: 0.283 AC: 4327 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.284 AC: 984 AN: 3470

East Asian (EAS) AF: 0.168 AC: 870 AN: 5182

South Asian (SAS) AF: 0.295 AC: 1419 AN: 4818

European-Finnish (FIN) AF: 0.505 AC: 5337 AN: 10562

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.397 AC: 27004 AN: 67992

Other (OTH) AF: 0.299 AC: 632 AN: 2114

Alfa AF: 0.333 Hom.: 3507

Asia WGS AF: 0.237 AC: 824 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	7.7
DANN	Benign	0.91
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs11014249; hg19: chr10-25111910;