chr1-109819060-C-A

Variant names:

• chr1-109819060-C-A
• rs499345

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 0.318 in 152,048 control chromosomes in the GnomAD database, including 8,265 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 0.32 (8265 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.270
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.403 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: 0.318 AC: 48238 AN: 151930 Hom.: 8252 Cov.: 32

Gnomad AFR AF: 0.408

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.0141

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.318 AC: 48283 AN: 152048 Hom.: 8265 Cov.: 32 AF XY: 0.315 AC XY: 23440 AN XY: 74316

African (AFR) AF: 0.408 AC: 16916 AN: 41426

American (AMR) AF: 0.252 AC: 3846 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.324 AC: 1123 AN: 3470

East Asian (EAS) AF: 0.0137 AC: 71 AN: 5182

South Asian (SAS) AF: 0.381 AC: 1834 AN: 4818

European-Finnish (FIN) AF: 0.260 AC: 2746 AN: 10580

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.303 AC: 20572 AN: 67968

Other (OTH) AF: 0.326 AC: 689 AN: 2114

Alfa AF: 0.310 Hom.: 12693

Bravo AF: 0.316

Asia WGS AF: 0.230 AC: 802 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.016
DANN	Benign	0.35
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs499345; hg19: chr1-110361682;