rs527430

Positions:

• chr1-47453149-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 0.0223 in 152,222 control chromosomes in the GnomAD database, including 102 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 0.022 (102 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.112 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.47453149G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0222 AC: 3384 AN: 152104 Hom.: 100 Cov.: 32

Gnomad AFR AF: 0.0470

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.00792

Gnomad ASJ AF: 0.00807

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.00996

Gnomad FIN AF: 0.00396

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00784

Gnomad OTH AF: 0.0196

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

GnomAD4 genome AF: 0.0223 AC: 3389 AN: 152222 Hom.: 102 Cov.: 32 AF XY: 0.0222 AC XY: 1656 AN XY: 74438

Gnomad4 AFR AF: 0.0471

Gnomad4 AMR AF: 0.00791

Gnomad4 ASJ AF: 0.00807

Gnomad4 EAS AF: 0.120

Gnomad4 SAS AF: 0.00956

Gnomad4 FIN AF: 0.00396

Gnomad4 NFE AF: 0.00784

Gnomad4 OTH AF: 0.0189

Alfa AF: 0.0101 Hom.: 70

Bravo AF: 0.0247

Asia WGS AF: 0.0570 AC: 199 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.71
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: rs527430; hg19: chr1-47918821;