chr1-47632734-A-G

Position:

• chr1-47632734-A-G

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;