chr5-84872006-T-C

Variant names:

• chr5-84872006-T-C
• rs4235662

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 0.239 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

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: 0.239 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

African (AFR) AF: 0.184 AC: 7657 AN: 41522

American (AMR) AF: 0.241 AC: 3689 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.239 AC: 830 AN: 3470

East Asian (EAS) AF: 0.222 AC: 1145 AN: 5168

South Asian (SAS) AF: 0.240 AC: 1156 AN: 4816

European-Finnish (FIN) AF: 0.293 AC: 3089 AN: 10558

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.264 AC: 17976 AN: 68000

Other (OTH) AF: 0.245 AC: 514 AN: 2098

Alfa AF: 0.259 Hom.: 5612

Bravo AF: 0.236

Asia WGS AF: 0.254 AC: 884 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.69
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs4235662; hg19: chr5-84167824;