1-202939708-A-C

Variant names:

• chr1-202939708-A-C
• rs10920531

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 0.565 in 151,860 control chromosomes in the GnomAD database, including 25,006 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 0.57 (25006 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.197
• Publications: 21 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.633 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.565 AC: 85801 AN: 151742 Hom.: 25003 Cov.: 31

Gnomad AFR AF: 0.455

Gnomad AMI AF: 0.543

Gnomad AMR AF: 0.559

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.680

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.638

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.565 AC: 85839 AN: 151860 Hom.: 25006 Cov.: 31 AF XY: 0.564 AC XY: 41856 AN XY: 74202

African (AFR) AF: 0.455 AC: 18832 AN: 41384

American (AMR) AF: 0.559 AC: 8523 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.595 AC: 2062 AN: 3468

East Asian (EAS) AF: 0.374 AC: 1931 AN: 5162

South Asian (SAS) AF: 0.437 AC: 2107 AN: 4822

European-Finnish (FIN) AF: 0.680 AC: 7160 AN: 10526

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.638 AC: 43311 AN: 67934

Other (OTH) AF: 0.587 AC: 1236 AN: 2104

Alfa AF: 0.613 Hom.: 26689

Bravo AF: 0.556

Asia WGS AF: 0.408 AC: 1418 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.0
DANN	Benign	0.57
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs10920531; hg19: chr1-202908836;