rs4885678

Variant names:

• chr13-79866356-G-T
• rs4885678

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 0.187 in 151,970 control chromosomes in the GnomAD database, including 2,874 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 0.19 (2874 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.419

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28399 AN: 151848 Hom.: 2877 Cov.: 32

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.283

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.0805

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.187 AC: 28420 AN: 151970 Hom.: 2874 Cov.: 32 AF XY: 0.186 AC XY: 13832 AN XY: 74292

Gnomad4 AFR AF: 0.261

Gnomad4 AMR AF: 0.218

Gnomad4 ASJ AF: 0.153

Gnomad4 EAS AF: 0.283

Gnomad4 SAS AF: 0.190

Gnomad4 FIN AF: 0.0805

Gnomad4 NFE AF: 0.147

Gnomad4 OTH AF: 0.189

Alfa AF: 0.156 Hom.: 1063

Bravo AF: 0.201

Asia WGS AF: 0.238 AC: 828 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.41
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4885678; hg19: chr13-80440491;