1-47453149-G-A

Variant names:

• chr1-47453149-G-A
• rs527430

Variant summary

Our verdict is Benign. The variant received -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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.0471 AC: 1954 AN: 41512

American (AMR) AF: 0.00791 AC: 121 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.00807 AC: 28 AN: 3470

East Asian (EAS) AF: 0.120 AC: 622 AN: 5184

South Asian (SAS) AF: 0.00956 AC: 46 AN: 4814

European-Finnish (FIN) AF: 0.00396 AC: 42 AN: 10614

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.00784 AC: 533 AN: 68012

Other (OTH) AF: 0.0189 AC: 40 AN: 2112

Alfa AF: 0.0126 Hom.: 172

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
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs527430; hg19: chr1-47918821;