5-136093331-A-G

Variant names:

• chr5-136093331-A-G
• rs7715300

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 0.152 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.307 AC: 12763 AN: 41508

American (AMR) AF: 0.102 AC: 1555 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 493 AN: 3472

East Asian (EAS) AF: 0.0931 AC: 482 AN: 5176

South Asian (SAS) AF: 0.0788 AC: 380 AN: 4824

European-Finnish (FIN) AF: 0.0603 AC: 640 AN: 10612

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.0936 AC: 6366 AN: 68018

Other (OTH) AF: 0.143 AC: 303 AN: 2112

Alfa AF: 0.110 Hom.: 3691

Bravo AF: 0.163

Asia WGS AF: 0.100 AC: 349 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.97
DANN	Benign	0.50
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs7715300; hg19: chr5-135429020;