rs280734

Positions:

• 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, non coding transcript 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: ENST00000453451.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.178

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000453451.5	n.180+47830G>A		intron_variant, non_coding_transcript_variant		4

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;