rs499345

Variant names:

• chr1-109819060-C-A
• rs499345

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.318 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

Gnomad4 AFR AF: 0.408

Gnomad4 AMR AF: 0.252

Gnomad4 ASJ AF: 0.324

Gnomad4 EAS AF: 0.0137

Gnomad4 SAS AF: 0.381

Gnomad4 FIN AF: 0.260

Gnomad4 NFE AF: 0.303

Gnomad4 OTH AF: 0.326

Alfa AF: 0.309 Hom.: 10021

Bravo AF: 0.316

Asia WGS AF: 0.230 AC: 802 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs499345; hg19: chr1-110361682;