13-77493346-G-C

Variant names:

• chr13-77493346-G-C
• rs4884068

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 0.196 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

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

African (AFR) AF: 0.141 AC: 5873 AN: 41506

American (AMR) AF: 0.242 AC: 3701 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.157 AC: 545 AN: 3472

East Asian (EAS) AF: 0.388 AC: 2010 AN: 5176

South Asian (SAS) AF: 0.243 AC: 1173 AN: 4828

European-Finnish (FIN) AF: 0.241 AC: 2543 AN: 10562

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.195 AC: 13228 AN: 67984

Other (OTH) AF: 0.208 AC: 440 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	5.6
DANN	Benign	0.53
PhyloP100		0.90

Splicing

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

Other links and lift over

dbSNP: rs4884068; hg19: chr13-78067481;