rs2182058

Variant names:

• chr13-33718980-T-A
• rs2182058
• ENST00000731018.1:n.194+18585T>A

Variant summary

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

The ENST00000731018.1(ENSG00000295576):​n.194+18585T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.059 in 152,224 control chromosomes in the GnomAD database, including 540 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 0.059 (540 hom., cov: 32)
• Consequence: ENSG00000295576 ENST00000731018.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.803
• Publications: 1 publications found

Genes affected

ENSG00000295576 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.237 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
ENSG00000295576	ENST00000731018.1	n.194+18585T>A		intron_variant	Intron 1 of 1
ENSG00000288767	ENST00000731141.1	n.50+39374T>A		intron_variant	Intron 1 of 1
ENSG00000295634	ENST00000731508.1	n.95+1975A>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0588 AC: 8950 AN: 152104 Hom.: 536 Cov.: 32

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0631

Gnomad ASJ AF: 0.0110

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.0489

Gnomad FIN AF: 0.0227

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0109

Gnomad OTH AF: 0.0507

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

GnomAD4 genome AF: 0.0590 AC: 8982 AN: 152224 Hom.: 540 Cov.: 32 AF XY: 0.0606 AC XY: 4511 AN XY: 74434

African (AFR) AF: 0.129 AC: 5353 AN: 41506

American (AMR) AF: 0.0634 AC: 970 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0110 AC: 38 AN: 3470

East Asian (EAS) AF: 0.249 AC: 1286 AN: 5174

South Asian (SAS) AF: 0.0485 AC: 234 AN: 4820

European-Finnish (FIN) AF: 0.0227 AC: 241 AN: 10616

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0109 AC: 743 AN: 68028

Other (OTH) AF: 0.0502 AC: 106 AN: 2112

Alfa AF: 0.0363 Hom.: 38

Bravo AF: 0.0673

Asia WGS AF: 0.173 AC: 600 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.4
DANN	Benign	0.76
PhyloP100		0.80

Splicing

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

Other links and lift over

dbSNP: rs2182058; hg19: chr13-34293117;