5-3689249-T-C

Variant names:

• chr5-3689249-T-C
• rs4866602

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 0.285 in 151,978 control chromosomes in the GnomAD database, including 6,780 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 0.28 (6780 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.87
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.541 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43245 AN: 151860 Hom.: 6760 Cov.: 32

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.558

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.285 AC: 43307 AN: 151978 Hom.: 6780 Cov.: 32 AF XY: 0.288 AC XY: 21378 AN XY: 74310

African (AFR) AF: 0.320 AC: 13245 AN: 41450

American (AMR) AF: 0.449 AC: 6864 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 745 AN: 3464

East Asian (EAS) AF: 0.558 AC: 2880 AN: 5164

South Asian (SAS) AF: 0.305 AC: 1470 AN: 4822

European-Finnish (FIN) AF: 0.207 AC: 2183 AN: 10548

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.221 AC: 15018 AN: 67938

Other (OTH) AF: 0.304 AC: 642 AN: 2114

Alfa AF: 0.251 Hom.: 10779

Bravo AF: 0.312

Asia WGS AF: 0.438 AC: 1519 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.093
DANN	Benign	0.46
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs4866602; hg19: chr5-3689363;