rs10205982

Variant names:

• chr2-48945289-G-A
• rs10205982
• ENST00000634588.1:n.303-927G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-48945289-G-A
• chr2-48945289-G-C

Variant summary

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

The ENST00000634588.1(ENSG00000282890):​n.303-927G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0436 in 152,274 control chromosomes in the GnomAD database, including 227 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 0.044 (227 hom., cov: 32)
• Consequence: ENSG00000282890 ENST00000634588.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 5 publications found

Genes affected

ENSG00000282890 (HGNC:58158):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0608 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
ENSG00000282890	ENST00000634588.1	n.303-927G>A		intron_variant	Intron 1 of 4	5

Frequencies

GnomAD3 genomes AF: 0.0437 AC: 6643 AN: 152156 Hom.: 227 Cov.: 32

Gnomad AFR AF: 0.0116

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.0472

Gnomad ASJ AF: 0.0718

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0147

Gnomad FIN AF: 0.0611

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0623

Gnomad OTH AF: 0.0464

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

GnomAD4 genome AF: 0.0436 AC: 6641 AN: 152274 Hom.: 227 Cov.: 32 AF XY: 0.0433 AC XY: 3227 AN XY: 74450

African (AFR) AF: 0.0116 AC: 480 AN: 41546

American (AMR) AF: 0.0471 AC: 721 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0718 AC: 249 AN: 3470

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5186

South Asian (SAS) AF: 0.0145 AC: 70 AN: 4822

European-Finnish (FIN) AF: 0.0611 AC: 648 AN: 10612

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0623 AC: 4239 AN: 68014

Other (OTH) AF: 0.0459 AC: 97 AN: 2112

Alfa AF: 0.0521 Hom.: 571

Bravo AF: 0.0418

Asia WGS AF: 0.00693 AC: 24 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.0060
DANN	Benign	0.37
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs10205982; hg19: chr2-49172428;