rs280734

Variant names:

• chr2-34879322-G-A
• rs280734
• ENST00000453451.5:n.180+47830G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-34879322-G-A
• chr2-34879322-G-C
• chr2-34879322-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000453451.5(ENSG00000226994):​n.180+47830G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.599 in 151,848 control chromosomes in the GnomAD database, including 28,403 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 0.60 (28403 hom., cov: 32)
• Consequence: ENSG00000226994 ENST00000453451.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.178

Genes affected

ENSG00000226994 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.754 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
ENSG00000226994	ENST00000453451.5	n.180+47830G>A		intron_variant	Intron 2 of 5	4
ENSG00000226994	ENST00000585391.5	n.115+47830G>A		intron_variant	Intron 1 of 5	5
ENSG00000226994	ENST00000586769.6	n.157+47830G>A		intron_variant	Intron 1 of 5	5

Frequencies

GnomAD3 genomes AF: 0.599 AC: 90825 AN: 151730 Hom.: 28356 Cov.: 32

Gnomad AFR AF: 0.760

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.417

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.612

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.556

Gnomad OTH AF: 0.573

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

GnomAD4 genome AF: 0.599 AC: 90928 AN: 151848 Hom.: 28403 Cov.: 32 AF XY: 0.598 AC XY: 44385 AN XY: 74224

Gnomad4 AFR AF: 0.761

Gnomad4 AMR AF: 0.417

Gnomad4 ASJ AF: 0.610

Gnomad4 EAS AF: 0.418

Gnomad4 SAS AF: 0.595

Gnomad4 FIN AF: 0.612

Gnomad4 NFE AF: 0.557

Gnomad4 OTH AF: 0.571

Alfa AF: 0.556 Hom.: 48247

Bravo AF: 0.586

Asia WGS AF: 0.498 AC: 1728 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs280734; hg19: chr2-35104389;