5-84872006-T-C

Position:

• chr5-84872006-T-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 0.239 in 152,120 control chromosomes in the GnomAD database, including 4,432 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 0.24 (4432 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.398

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 (NFE) allele frequency at 95% confidence interval = 0.261 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: 0.239 AC: 36372 AN: 152000 Hom.: 4425 Cov.: 32

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.239 AC: 36404 AN: 152120 Hom.: 4432 Cov.: 32 AF XY: 0.240 AC XY: 17853 AN XY: 74354

Gnomad4 AFR AF: 0.184

Gnomad4 AMR AF: 0.241

Gnomad4 ASJ AF: 0.239

Gnomad4 EAS AF: 0.222

Gnomad4 SAS AF: 0.240

Gnomad4 FIN AF: 0.293

Gnomad4 NFE AF: 0.264

Gnomad4 OTH AF: 0.245

Alfa AF: 0.260 Hom.: 4858

Bravo AF: 0.236

Asia WGS AF: 0.254 AC: 884 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4235662; hg19: chr5-84167824;