5-136028186-A-G

Position:

• chr5-136028186-A-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 0.588 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.587 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

Gnomad4 AFR AF: 0.818

Gnomad4 AMR AF: 0.566

Gnomad4 ASJ AF: 0.482

Gnomad4 EAS AF: 0.612

Gnomad4 SAS AF: 0.511

Gnomad4 FIN AF: 0.534

Gnomad4 NFE AF: 0.473

Gnomad4 OTH AF: 0.572

Alfa AF: 0.490 Hom.: 18751

Bravo AF: 0.601

Asia WGS AF: 0.598 AC: 2076 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2282790; hg19: chr5-135363875;