5-13088300-C-G

Position:

• chr5-13088300-C-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 0.69 in 152,030 control chromosomes in the GnomAD database, including 37,819 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 0.69 (37819 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.835

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 (EAS) allele frequency at 95% confidence interval = 0.882 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: 0.690 AC: 104817 AN: 151912 Hom.: 37767 Cov.: 32

Gnomad AFR AF: 0.890

Gnomad AMI AF: 0.643

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.895

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.715

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.578

Gnomad OTH AF: 0.671

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

GnomAD4 genome AF: 0.690 AC: 104926 AN: 152030 Hom.: 37819 Cov.: 32 AF XY: 0.694 AC XY: 51532 AN XY: 74280

Gnomad4 AFR AF: 0.890

Gnomad4 AMR AF: 0.613

Gnomad4 ASJ AF: 0.602

Gnomad4 EAS AF: 0.895

Gnomad4 SAS AF: 0.608

Gnomad4 FIN AF: 0.715

Gnomad4 NFE AF: 0.578

Gnomad4 OTH AF: 0.670

Alfa AF: 0.552 Hom.: 1749

Bravo AF: 0.690

Asia WGS AF: 0.721 AC: 2503 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.34
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1840870; hg19: chr5-13088412;