rs2082107

Variant names:

• chr10-43073058-A-G
• rs2082107
• ENST00000794440.1:n.52-1547T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000794440.1(ENSG00000303432):​n.52-1547T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 151,942 control chromosomes in the GnomAD database, including 14,490 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 (14490 hom., cov: 32)
• Consequence: ENSG00000303432 ENST00000794440.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.736
• Publications: 0 publications found

Genes affected

ENSG00000303432 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.476 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
ENSG00000303432	ENST00000794440.1	n.52-1547T>C		intron_variant	Intron 1 of 2
ENSG00000303432	ENST00000794441.1	n.117-1547T>C		intron_variant	Intron 1 of 3
ENSG00000303432	ENST00000794442.1	n.108-1547T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.435 AC: 66013 AN: 151824 Hom.: 14463 Cov.: 32

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.421

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

GnomAD4 genome AF: 0.435 AC: 66090 AN: 151942 Hom.: 14490 Cov.: 32 AF XY: 0.434 AC XY: 32211 AN XY: 74246

African (AFR) AF: 0.482 AC: 19976 AN: 41448

American (AMR) AF: 0.456 AC: 6970 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.342 AC: 1187 AN: 3466

East Asian (EAS) AF: 0.318 AC: 1640 AN: 5150

South Asian (SAS) AF: 0.423 AC: 2037 AN: 4812

European-Finnish (FIN) AF: 0.381 AC: 4013 AN: 10546

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.424 AC: 28808 AN: 67930

Other (OTH) AF: 0.423 AC: 891 AN: 2108

Alfa AF: 0.425 Hom.: 1710

Bravo AF: 0.444

Asia WGS AF: 0.373 AC: 1297 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.1
DANN	Benign	0.56
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs2082107; hg19: chr10-43568506;