1-56851886-A-G

Variant names:

• chr1-56851886-A-G
• rs10489623

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.133 in 149,794 control chromosomes in the GnomAD database, including 1,823 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 0.13 (1823 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.362
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.367 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.132 AC: 19828 AN: 149716 Hom.: 1813 Cov.: 32

Gnomad AFR AF: 0.0456

Gnomad AMI AF: 0.0527

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.0860

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.133 AC: 19859 AN: 149794 Hom.: 1823 Cov.: 32 AF XY: 0.141 AC XY: 10282 AN XY: 73060

African (AFR) AF: 0.0457 AC: 1838 AN: 40210

American (AMR) AF: 0.269 AC: 4063 AN: 15106

Ashkenazi Jewish (ASJ) AF: 0.111 AC: 384 AN: 3460

East Asian (EAS) AF: 0.381 AC: 1920 AN: 5036

South Asian (SAS) AF: 0.158 AC: 756 AN: 4788

European-Finnish (FIN) AF: 0.200 AC: 2029 AN: 10150

Middle Eastern (MID) AF: 0.0966 AC: 28 AN: 290

European-Non Finnish (NFE) AF: 0.126 AC: 8525 AN: 67758

Other (OTH) AF: 0.128 AC: 268 AN: 2086

Alfa AF: 0.129 Hom.: 2482

Bravo AF: 0.134

Asia WGS AF: 0.223 AC: 757 AN: 3402

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	8.7
DANN	Benign	0.74
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs10489623; hg19: chr1-57317559;