rs1456017

Positions:

• chr2-46680488-C-G
• chr2-46680488-C-T

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 0.521 in 151,828 control chromosomes in the GnomAD database, including 21,111 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 0.52 (21111 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.119

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.627 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.46680488C>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.521 AC: 79053 AN: 151710 Hom.: 21107 Cov.: 31

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.709

Gnomad AMR AF: 0.637

Gnomad ASJ AF: 0.669

Gnomad EAS AF: 0.645

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.539

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.521 AC: 79081 AN: 151828 Hom.: 21111 Cov.: 31 AF XY: 0.524 AC XY: 38886 AN XY: 74210

Gnomad4 AFR AF: 0.422

Gnomad4 AMR AF: 0.637

Gnomad4 ASJ AF: 0.669

Gnomad4 EAS AF: 0.645

Gnomad4 SAS AF: 0.598

Gnomad4 FIN AF: 0.451

Gnomad4 NFE AF: 0.539

Gnomad4 OTH AF: 0.565

Alfa AF: 0.503 Hom.: 2418

Bravo AF: 0.533

Asia WGS AF: 0.620 AC: 2154 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.2
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1456017; hg19: chr2-46907627;