chr1-4506735-A-G

Variant names:

• chr1-4506735-A-G
• rs1870509

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 0.582 in 151,984 control chromosomes in the GnomAD database, including 26,073 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 0.58 (26073 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.83 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: 0.582 AC: 88427 AN: 151866 Hom.: 26045 Cov.: 32

Gnomad AFR AF: 0.586

Gnomad AMI AF: 0.673

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.573

Gnomad EAS AF: 0.850

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.531

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.545

Gnomad OTH AF: 0.612

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

GnomAD4 genome AF: 0.582 AC: 88505 AN: 151984 Hom.: 26073 Cov.: 32 AF XY: 0.584 AC XY: 43416 AN XY: 74284

African (AFR) AF: 0.586 AC: 24279 AN: 41442

American (AMR) AF: 0.683 AC: 10442 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.573 AC: 1987 AN: 3466

East Asian (EAS) AF: 0.851 AC: 4383 AN: 5152

South Asian (SAS) AF: 0.565 AC: 2712 AN: 4804

European-Finnish (FIN) AF: 0.531 AC: 5605 AN: 10562

Middle Eastern (MID) AF: 0.562 AC: 164 AN: 292

European-Non Finnish (NFE) AF: 0.545 AC: 37029 AN: 67970

Other (OTH) AF: 0.613 AC: 1292 AN: 2106

Alfa AF: 0.539 Hom.: 15024

Bravo AF: 0.599

Asia WGS AF: 0.685 AC: 2384 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.016
DANN	Benign	0.24
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs1870509; hg19: chr1-4566795; COSMIC: COSV59919793;