rs17542930

Variant names:

• chr2-48859145-T-C
• rs17542930
• ENST00000634588.1:n.302+49504T>C

Your query was ambiguous. Multiple possible variants found:

• chr2-48859145-T-C
• chr2-48859145-T-G

Variant summary

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

The ENST00000634588.1(ENSG00000282890):​n.302+49504T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 152,260 control chromosomes in the GnomAD database, including 1,237 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 0.11 (1237 hom., cov: 33)
• Consequence: ENSG00000282890 ENST00000634588.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.688
• Publications: 1 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.176 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.302+49504T>C		intron_variant	Intron 1 of 4	5

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17353 AN: 152142 Hom.: 1238 Cov.: 33

Gnomad AFR AF: 0.0401

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.0955

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.114 AC: 17343 AN: 152260 Hom.: 1237 Cov.: 33 AF XY: 0.117 AC XY: 8721 AN XY: 74454

African (AFR) AF: 0.0400 AC: 1662 AN: 41554

American (AMR) AF: 0.0954 AC: 1460 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 613 AN: 3470

East Asian (EAS) AF: 0.185 AC: 962 AN: 5192

South Asian (SAS) AF: 0.150 AC: 721 AN: 4822

European-Finnish (FIN) AF: 0.197 AC: 2084 AN: 10592

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.140 AC: 9488 AN: 68010

Other (OTH) AF: 0.117 AC: 247 AN: 2114

Alfa AF: 0.0795 Hom.: 145

Bravo AF: 0.105

Asia WGS AF: 0.132 AC: 457 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.11
DANN	Benign	0.31
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs17542930; hg19: chr2-49086284;