rs36058922

Positions:

• chr5-18608300-T-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 0.15 in 151,922 control chromosomes in the GnomAD database, including 2,096 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 0.15 (2096 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0440

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22797 AN: 151804 Hom.: 2094 Cov.: 32

Gnomad AFR AF: 0.0456

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.150 AC: 22790 AN: 151922 Hom.: 2096 Cov.: 32 AF XY: 0.153 AC XY: 11377 AN XY: 74252

Gnomad4 AFR AF: 0.0455

Gnomad4 AMR AF: 0.213

Gnomad4 ASJ AF: 0.160

Gnomad4 EAS AF: 0.113

Gnomad4 SAS AF: 0.233

Gnomad4 FIN AF: 0.186

Gnomad4 NFE AF: 0.189

Gnomad4 OTH AF: 0.175

Alfa AF: 0.167 Hom.: 337

Bravo AF: 0.144

Asia WGS AF: 0.152 AC: 532 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.6
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs36058922; hg19: chr5-18608409;