chr13-78701658-A-G

Position:

• chr13-78701658-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 0.0859 in 152,268 control chromosomes in the GnomAD database, including 576 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 0.086 (576 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.263

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.111 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0860 AC: 13083 AN: 152150 Hom.: 577 Cov.: 32

Gnomad AFR AF: 0.0761

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.0901

Gnomad SAS AF: 0.0608

Gnomad FIN AF: 0.0493

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0898

Gnomad OTH AF: 0.0950

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

GnomAD4 genome AF: 0.0859 AC: 13081 AN: 152268 Hom.: 576 Cov.: 32 AF XY: 0.0837 AC XY: 6231 AN XY: 74456

Gnomad4 AFR AF: 0.0759

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.101

Gnomad4 EAS AF: 0.0901

Gnomad4 SAS AF: 0.0608

Gnomad4 FIN AF: 0.0493

Gnomad4 NFE AF: 0.0898

Gnomad4 OTH AF: 0.0931

Alfa AF: 0.0946 Hom.: 691

Bravo AF: 0.0927

Asia WGS AF: 0.0690 AC: 238 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.5
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1359536; hg19: chr13-79275793;