5-136369986-G-A

Position:

• chr5-136369986-G-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 0.377 in 151,898 control chromosomes in the GnomAD database, including 11,710 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 0.38 (11710 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0550

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.543 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: 0.376 AC: 57127 AN: 151778 Hom.: 11675 Cov.: 31

Gnomad AFR AF: 0.548

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.377 AC: 57216 AN: 151898 Hom.: 11710 Cov.: 31 AF XY: 0.371 AC XY: 27529 AN XY: 74248

Gnomad4 AFR AF: 0.549

Gnomad4 AMR AF: 0.313

Gnomad4 ASJ AF: 0.381

Gnomad4 EAS AF: 0.421

Gnomad4 SAS AF: 0.208

Gnomad4 FIN AF: 0.303

Gnomad4 NFE AF: 0.306

Gnomad4 OTH AF: 0.370

Alfa AF: 0.321 Hom.: 16816

Bravo AF: 0.394

Asia WGS AF: 0.339 AC: 1182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.15
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2673925; hg19: chr5-135705674;