5-136028186-A-G

Variant names:

• chr5-136028186-A-G
• rs2282790

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 0.588 in 152,110 control chromosomes in the GnomAD database, including 28,066 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 0.59 (28066 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.170
• Publications: 12 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.811 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.587 AC: 89286 AN: 151992 Hom.: 28009 Cov.: 33

Gnomad AFR AF: 0.818

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.482

Gnomad EAS AF: 0.611

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.455

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.588 AC: 89412 AN: 152110 Hom.: 28066 Cov.: 33 AF XY: 0.588 AC XY: 43699 AN XY: 74352

African (AFR) AF: 0.818 AC: 33957 AN: 41522

American (AMR) AF: 0.566 AC: 8648 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.482 AC: 1671 AN: 3468

East Asian (EAS) AF: 0.612 AC: 3150 AN: 5150

South Asian (SAS) AF: 0.511 AC: 2466 AN: 4822

European-Finnish (FIN) AF: 0.534 AC: 5651 AN: 10576

Middle Eastern (MID) AF: 0.483 AC: 141 AN: 292

European-Non Finnish (NFE) AF: 0.473 AC: 32177 AN: 67972

Other (OTH) AF: 0.572 AC: 1209 AN: 2114

Alfa AF: 0.507 Hom.: 28889

Bravo AF: 0.601

Asia WGS AF: 0.598 AC: 2076 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.7
DANN	Benign	0.64
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs2282790; hg19: chr5-135363875;