10-71049809-T-C

Variant names:

• chr10-71049809-T-C
• rs7090828
• ENST00000646051.1:n.392+23097T>C

Variant summary

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

The ENST00000646051.1(ENSG00000285300):​n.392+23097T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.611 in 151,804 control chromosomes in the GnomAD database, including 29,197 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 0.61 (29197 hom., cov: 30)
• Consequence: ENSG00000285300 ENST00000646051.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.565

Genes affected

ENSG00000285300 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.771 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
ENSG00000285300	ENST00000646051.1	n.392+23097T>C		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.611 AC: 92635 AN: 151686 Hom.: 29161 Cov.: 30

Gnomad AFR AF: 0.779

Gnomad AMI AF: 0.717

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.678

Gnomad SAS AF: 0.649

Gnomad FIN AF: 0.502

Gnomad MID AF: 0.567

Gnomad NFE AF: 0.543

Gnomad OTH AF: 0.574

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

GnomAD4 genome AF: 0.611 AC: 92713 AN: 151804 Hom.: 29197 Cov.: 30 AF XY: 0.608 AC XY: 45126 AN XY: 74188

Gnomad4 AFR AF: 0.778

Gnomad4 AMR AF: 0.507

Gnomad4 ASJ AF: 0.556

Gnomad4 EAS AF: 0.679

Gnomad4 SAS AF: 0.650

Gnomad4 FIN AF: 0.502

Gnomad4 NFE AF: 0.543

Gnomad4 OTH AF: 0.576

Alfa AF: 0.550 Hom.: 23061

Bravo AF: 0.616

Asia WGS AF: 0.655 AC: 2277 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.6
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7090828; hg19: chr10-72809566;