5-135016844-C-T

Variant names:

• chr5-135016844-C-T
• rs28330

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 0.402 in 152,088 control chromosomes in the GnomAD database, including 13,092 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 0.40 (13092 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.386
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.605 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: 0.402 AC: 61017 AN: 151970 Hom.: 13063 Cov.: 33

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.510

Gnomad AMR AF: 0.518

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.624

Gnomad SAS AF: 0.599

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.402 AC: 61067 AN: 152088 Hom.: 13092 Cov.: 33 AF XY: 0.405 AC XY: 30141 AN XY: 74358

African (AFR) AF: 0.280 AC: 11624 AN: 41502

American (AMR) AF: 0.519 AC: 7937 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.353 AC: 1226 AN: 3470

East Asian (EAS) AF: 0.623 AC: 3219 AN: 5170

South Asian (SAS) AF: 0.599 AC: 2881 AN: 4812

European-Finnish (FIN) AF: 0.386 AC: 4079 AN: 10580

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.423 AC: 28731 AN: 67954

Other (OTH) AF: 0.393 AC: 830 AN: 2114

Alfa AF: 0.418 Hom.: 51826

Bravo AF: 0.402

Asia WGS AF: 0.619 AC: 2149 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.8
DANN	Benign	0.67
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs28330; hg19: chr5-134352534; COSMIC: COSV60199531;