1-47632734-A-G

Variant names:

• chr1-47632734-A-G
• rs2506991

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 0.458 in 151,942 control chromosomes in the GnomAD database, including 16,590 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 0.46 (16590 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.558 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: 0.458 AC: 69514 AN: 151824 Hom.: 16584 Cov.: 31

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.590

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.585

Gnomad EAS AF: 0.437

Gnomad SAS AF: 0.484

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.506

Gnomad OTH AF: 0.473

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

GnomAD4 genome AF: 0.458 AC: 69560 AN: 151942 Hom.: 16590 Cov.: 31 AF XY: 0.460 AC XY: 34142 AN XY: 74240

Gnomad4 AFR AF: 0.325

Gnomad4 AMR AF: 0.568

Gnomad4 ASJ AF: 0.585

Gnomad4 EAS AF: 0.438

Gnomad4 SAS AF: 0.483

Gnomad4 FIN AF: 0.447

Gnomad4 NFE AF: 0.506

Gnomad4 OTH AF: 0.470

Alfa AF: 0.507 Hom.: 26221

Bravo AF: 0.460

Asia WGS AF: 0.467 AC: 1620 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.4
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2506991; hg19: chr1-48098406;