rs2059849

Variant names:

• chr5-67315082-T-C
• rs2059849

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 0.242 in 152,188 control chromosomes in the GnomAD database, including 7,524 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 0.24 (7524 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.554 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: 0.241 AC: 36725 AN: 152072 Hom.: 7494 Cov.: 33

Gnomad AFR AF: 0.560

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.0905

Gnomad EAS AF: 0.0229

Gnomad SAS AF: 0.0443

Gnomad FIN AF: 0.0876

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.242 AC: 36804 AN: 152188 Hom.: 7524 Cov.: 33 AF XY: 0.232 AC XY: 17296 AN XY: 74420

Gnomad4 AFR AF: 0.560

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.0905

Gnomad4 EAS AF: 0.0229

Gnomad4 SAS AF: 0.0440

Gnomad4 FIN AF: 0.0876

Gnomad4 NFE AF: 0.135

Gnomad4 OTH AF: 0.205

Alfa AF: 0.136 Hom.: 3274

Bravo AF: 0.260

Asia WGS AF: 0.0680 AC: 238 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.1
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2059849; hg19: chr5-66610910; COSMIC: COSV60150099;