rs30328

Variant names:

• chr5-148786884-C-T
• rs30328

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 0.458 in 151,942 control chromosomes in the GnomAD database, including 16,232 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 0.46 (16232 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.377
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.485 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: 0.458 AC: 69603 AN: 151824 Hom.: 16221 Cov.: 32

Gnomad AFR AF: 0.442

Gnomad AMI AF: 0.420

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.549

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.479

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.486

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

GnomAD4 genome AF: 0.458 AC: 69650 AN: 151942 Hom.: 16232 Cov.: 32 AF XY: 0.456 AC XY: 33897 AN XY: 74256

African (AFR) AF: 0.442 AC: 18297 AN: 41424

American (AMR) AF: 0.495 AC: 7553 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.549 AC: 1905 AN: 3470

East Asian (EAS) AF: 0.318 AC: 1640 AN: 5156

South Asian (SAS) AF: 0.480 AC: 2314 AN: 4820

European-Finnish (FIN) AF: 0.393 AC: 4136 AN: 10536

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.474 AC: 32203 AN: 67950

Other (OTH) AF: 0.488 AC: 1031 AN: 2114

Alfa AF: 0.466 Hom.: 11357

Bravo AF: 0.463

Asia WGS AF: 0.420 AC: 1461 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.8
DANN	Benign	0.50
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs30328; hg19: chr5-148166447;