chr2-15583481-G-A

Position:

• chr2-15583481-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 0.661 in 149,512 control chromosomes in the GnomAD database, including 32,536 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 0.66 (32536 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.617

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.766 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.15583481G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.661 AC: 98719 AN: 149400 Hom.: 32513 Cov.: 32

Gnomad AFR AF: 0.773

Gnomad AMI AF: 0.620

Gnomad AMR AF: 0.666

Gnomad ASJ AF: 0.607

Gnomad EAS AF: 0.729

Gnomad SAS AF: 0.751

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.634

Gnomad NFE AF: 0.606

Gnomad OTH AF: 0.638

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

GnomAD4 genome AF: 0.661 AC: 98798 AN: 149512 Hom.: 32536 Cov.: 32 AF XY: 0.658 AC XY: 48011 AN XY: 72944

Gnomad4 AFR AF: 0.773

Gnomad4 AMR AF: 0.666

Gnomad4 ASJ AF: 0.607

Gnomad4 EAS AF: 0.729

Gnomad4 SAS AF: 0.751

Gnomad4 FIN AF: 0.530

Gnomad4 NFE AF: 0.606

Gnomad4 OTH AF: 0.638

Alfa AF: 0.601 Hom.: 10915

Bravo AF: 0.661

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.074
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2890489; hg19: chr2-15723605;