chr1-47632734-A-G

Variant names:

• chr1-47632734-A-G
• rs2506991

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 0.458 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.325 AC: 13471 AN: 41458

American (AMR) AF: 0.568 AC: 8669 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.585 AC: 2032 AN: 3472

East Asian (EAS) AF: 0.438 AC: 2247 AN: 5136

South Asian (SAS) AF: 0.483 AC: 2319 AN: 4804

European-Finnish (FIN) AF: 0.447 AC: 4717 AN: 10554

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.506 AC: 34407 AN: 67948

Other (OTH) AF: 0.470 AC: 988 AN: 2102

Alfa AF: 0.500 Hom.: 35684

Bravo AF: 0.460

Asia WGS AF: 0.467 AC: 1620 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.4
DANN	Benign	0.69
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs2506991; hg19: chr1-48098406;