rs1878526

Positions:

• chr2-118281022-G-A

Variant summary

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

The variant allele was found at a frequency of 0.242 in 152,012 control chromosomes in the GnomAD database, including 4,742 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 0.24 (4742 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.493

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.118281022G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36694 AN: 151896 Hom.: 4728 Cov.: 33

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.242 AC: 36736 AN: 152012 Hom.: 4742 Cov.: 33 AF XY: 0.239 AC XY: 17782 AN XY: 74290

Gnomad4 AFR AF: 0.324

Gnomad4 AMR AF: 0.190

Gnomad4 ASJ AF: 0.195

Gnomad4 EAS AF: 0.355

Gnomad4 SAS AF: 0.257

Gnomad4 FIN AF: 0.141

Gnomad4 NFE AF: 0.211

Gnomad4 OTH AF: 0.225

Alfa AF: 0.216 Hom.: 6110

Bravo AF: 0.246

Asia WGS AF: 0.277 AC: 961 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	11
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1878526; hg19: chr2-119038598; COSMIC: COSV50679589;