rs2658161

Variant names:

• chr5-8133581-T-C
• rs2658161

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 0.0558 in 152,038 control chromosomes in the GnomAD database, including 273 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 0.056 (273 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.445

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 (NFE) allele frequency at 95% confidence interval = 0.0605 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: 0.0558 AC: 8477 AN: 151922 Hom.: 274 Cov.: 32

Gnomad AFR AF: 0.0588

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.0535

Gnomad ASJ AF: 0.0484

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0232

Gnomad FIN AF: 0.0439

Gnomad MID AF: 0.0764

Gnomad NFE AF: 0.0621

Gnomad OTH AF: 0.0560

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

GnomAD4 genome AF: 0.0558 AC: 8485 AN: 152038 Hom.: 273 Cov.: 32 AF XY: 0.0537 AC XY: 3991 AN XY: 74334

Gnomad4 AFR AF: 0.0588

Gnomad4 AMR AF: 0.0534

Gnomad4 ASJ AF: 0.0484

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0230

Gnomad4 FIN AF: 0.0439

Gnomad4 NFE AF: 0.0621

Gnomad4 OTH AF: 0.0555

Alfa AF: 0.0640 Hom.: 416

Bravo AF: 0.0583

Asia WGS AF: 0.0170 AC: 58 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.0
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2658161; hg19: chr5-8133694;