rs2099082

Variant names:

• chr5-54899963-T-C
• rs2099082

Your query was ambiguous. Multiple possible variants found:

• chr5-54899963-T-C
• chr5-54899963-T-G

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 0.201 in 152,158 control chromosomes in the GnomAD database, including 3,907 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 0.20 (3907 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.42 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: 0.201 AC: 30587 AN: 152040 Hom.: 3904 Cov.: 32

Gnomad AFR AF: 0.0702

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.437

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.201 AC: 30588 AN: 152158 Hom.: 3907 Cov.: 32 AF XY: 0.210 AC XY: 15631 AN XY: 74370

Gnomad4 AFR AF: 0.0700

Gnomad4 AMR AF: 0.338

Gnomad4 ASJ AF: 0.216

Gnomad4 EAS AF: 0.435

Gnomad4 SAS AF: 0.315

Gnomad4 FIN AF: 0.286

Gnomad4 NFE AF: 0.211

Gnomad4 OTH AF: 0.211

Alfa AF: 0.231 Hom.: 814

Bravo AF: 0.199

Asia WGS AF: 0.369 AC: 1283 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.087
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2099082; hg19: chr5-54195791;