chr5-136093331-A-G

Position:

• chr5-136093331-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 0.152 in 152,214 control chromosomes in the GnomAD database, including 2,496 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 (2496 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.151

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.303 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: 0.152 AC: 23115 AN: 152096 Hom.: 2491 Cov.: 33

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.0927

Gnomad SAS AF: 0.0781

Gnomad FIN AF: 0.0603

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0936

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.152 AC: 23153 AN: 152214 Hom.: 2496 Cov.: 33 AF XY: 0.147 AC XY: 10966 AN XY: 74428

Gnomad4 AFR AF: 0.307

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.142

Gnomad4 EAS AF: 0.0931

Gnomad4 SAS AF: 0.0788

Gnomad4 FIN AF: 0.0603

Gnomad4 NFE AF: 0.0936

Gnomad4 OTH AF: 0.143

Alfa AF: 0.0956 Hom.: 1060

Bravo AF: 0.163

Asia WGS AF: 0.100 AC: 349 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.97
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7715300; hg19: chr5-135429020;