5-2409874-T-C

Variant names:

• chr5-2409874-T-C
• rs4866482

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 0.306 in 151,954 control chromosomes in the GnomAD database, including 7,525 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 0.31 (7525 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.245
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.395 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: 0.306 AC: 46531 AN: 151836 Hom.: 7510 Cov.: 32

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.306 AC: 46573 AN: 151954 Hom.: 7525 Cov.: 32 AF XY: 0.308 AC XY: 22886 AN XY: 74254

African (AFR) AF: 0.400 AC: 16566 AN: 41404

American (AMR) AF: 0.255 AC: 3891 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.297 AC: 1031 AN: 3472

East Asian (EAS) AF: 0.209 AC: 1079 AN: 5162

South Asian (SAS) AF: 0.352 AC: 1696 AN: 4812

European-Finnish (FIN) AF: 0.287 AC: 3035 AN: 10558

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.272 AC: 18461 AN: 67964

Other (OTH) AF: 0.281 AC: 592 AN: 2106

Alfa AF: 0.283 Hom.: 20251

Bravo AF: 0.302

Asia WGS AF: 0.298 AC: 1035 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	4.2
DANN	Benign	0.68
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs4866482; hg19: chr5-2409988;