chr5-84941243-C-T

Variant names:

• chr5-84941243-C-T
• rs12518285

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 0.214 in 151,618 control chromosomes in the GnomAD database, including 3,771 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 0.21 (3771 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.421
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.214 AC: 32441 AN: 151498 Hom.: 3772 Cov.: 32

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.242

Gnomad MID AF: 0.245

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.214 AC: 32445 AN: 151618 Hom.: 3771 Cov.: 32 AF XY: 0.216 AC XY: 15995 AN XY: 74070

African (AFR) AF: 0.115 AC: 4766 AN: 41438

American (AMR) AF: 0.251 AC: 3814 AN: 15168

Ashkenazi Jewish (ASJ) AF: 0.243 AC: 844 AN: 3468

East Asian (EAS) AF: 0.199 AC: 1024 AN: 5152

South Asian (SAS) AF: 0.300 AC: 1441 AN: 4810

European-Finnish (FIN) AF: 0.242 AC: 2543 AN: 10492

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.255 AC: 17314 AN: 67782

Other (OTH) AF: 0.201 AC: 423 AN: 2104

Alfa AF: 0.244 Hom.: 6209

Bravo AF: 0.202

Asia WGS AF: 0.236 AC: 820 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.0
DANN	Benign	0.62
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs12518285; hg19: chr5-84237061;