rs1504155

chr2-49175111-A-Cchr2-49175111-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000634588.1(ENSG00000282890):n.492+228706A>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.466 in 152,042 control chromosomes in the GnomAD database, including 16,939 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 0.47 (16939 hom., cov: 33)
• Consequence: ENST00000634588.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.188

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.46).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000634588.1	n.492+228706A>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.466 AC: 70868 AN: 151924 Hom.: 16928 Cov.: 33

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.518

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.588

Gnomad SAS AF: 0.568

Gnomad FIN AF: 0.520

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.506

Gnomad OTH AF: 0.476

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

GnomAD4 genome AF: 0.466 AC: 70926 AN: 152042 Hom.: 16939 Cov.: 33 AF XY: 0.470 AC XY: 34957 AN XY: 74320

Gnomad4 AFR AF: 0.344

Gnomad4 AMR AF: 0.519

Gnomad4 ASJ AF: 0.444

Gnomad4 EAS AF: 0.587

Gnomad4 SAS AF: 0.566

Gnomad4 FIN AF: 0.520

Gnomad4 NFE AF: 0.506

Gnomad4 OTH AF: 0.479

Alfa AF: 0.472 Hom.: 3352

Bravo AF: 0.462

Asia WGS AF: 0.563 AC: 1957 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.46
Cadd	Benign	15
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1504155; hg19: chr2-49402250;