1-56851886-A-G

Variant names:

• chr1-56851886-A-G
• rs10489623

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.132 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

Gnomad4 AFR AF: 0.0457

Gnomad4 AMR AF: 0.269

Gnomad4 ASJ AF: 0.111

Gnomad4 EAS AF: 0.381

Gnomad4 SAS AF: 0.158

Gnomad4 FIN AF: 0.200

Gnomad4 NFE AF: 0.126

Gnomad4 OTH AF: 0.128

Alfa AF: 0.128 Hom.: 1921

Bravo AF: 0.134

Asia WGS AF: 0.223 AC: 757 AN: 3402

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10489623; hg19: chr1-57317559;