rs36058922

Variant names:

• chr5-18608300-T-A
• rs36058922

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.0455 AC: 1888 AN: 41490

American (AMR) AF: 0.213 AC: 3236 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.160 AC: 554 AN: 3466

East Asian (EAS) AF: 0.113 AC: 583 AN: 5148

South Asian (SAS) AF: 0.233 AC: 1123 AN: 4820

European-Finnish (FIN) AF: 0.186 AC: 1971 AN: 10578

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.189 AC: 12815 AN: 67894

Other (OTH) AF: 0.175 AC: 369 AN: 2110

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
PhyloP100		0.044

Splicing

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

Other links and lift over

dbSNP: rs36058922; hg19: chr5-18608409;