13-77493346-G-C

Position:

• chr13-77493346-G-C

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 0.196 in 152,130 control chromosomes in the GnomAD database, including 3,168 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 0.20 (3168 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.900

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.374 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: 0.196 AC: 29849 AN: 152012 Hom.: 3168 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.208

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

GnomAD4 genome AF: 0.196 AC: 29852 AN: 152130 Hom.: 3168 Cov.: 32 AF XY: 0.199 AC XY: 14834 AN XY: 74378

Gnomad4 AFR AF: 0.141

Gnomad4 AMR AF: 0.242

Gnomad4 ASJ AF: 0.157

Gnomad4 EAS AF: 0.388

Gnomad4 SAS AF: 0.243

Gnomad4 FIN AF: 0.241

Gnomad4 NFE AF: 0.195

Gnomad4 OTH AF: 0.208

Alfa AF: 0.0635 Hom.: 72

Bravo AF: 0.194

Asia WGS AF: 0.308 AC: 1069 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	5.6
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4884068; hg19: chr13-78067481;