rs499345

chr1-109819060-C-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;