rs6882300

chr5-175449424-A-T

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 0.0712 in 152,196 control chromosomes in the GnomAD database, including 748 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 0.071 (748 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.703

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.191 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: 0.0712 AC: 10832 AN: 152078 Hom.: 746 Cov.: 33

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0506

Gnomad ASJ AF: 0.0248

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.0193

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0154

Gnomad OTH AF: 0.0627

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

GnomAD4 genome AF: 0.0712 AC: 10843 AN: 152196 Hom.: 748 Cov.: 33 AF XY: 0.0712 AC XY: 5295 AN XY: 74418

Gnomad4 AFR AF: 0.169

Gnomad4 AMR AF: 0.0504

Gnomad4 ASJ AF: 0.0248

Gnomad4 EAS AF: 0.201

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.0193

Gnomad4 NFE AF: 0.0154

Gnomad4 OTH AF: 0.0649

Alfa AF: 0.0480 Hom.: 55

Bravo AF: 0.0787

Asia WGS AF: 0.169 AC: 588 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	7.3
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6882300; hg19: chr5-174876427;