rs30329

Variant names:

• chr5-148788271-T-C
• rs30329

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 0.558 in 152,120 control chromosomes in the GnomAD database, including 24,559 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 0.56 (24559 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.695 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: 0.558 AC: 84793 AN: 152002 Hom.: 24519 Cov.: 33

Gnomad AFR AF: 0.702

Gnomad AMI AF: 0.428

Gnomad AMR AF: 0.552

Gnomad ASJ AF: 0.603

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.558

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.506

Gnomad OTH AF: 0.575

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

GnomAD4 genome AF: 0.558 AC: 84888 AN: 152120 Hom.: 24559 Cov.: 33 AF XY: 0.554 AC XY: 41185 AN XY: 74362

African (AFR) AF: 0.702 AC: 29125 AN: 41480

American (AMR) AF: 0.552 AC: 8437 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.603 AC: 2095 AN: 3472

East Asian (EAS) AF: 0.382 AC: 1982 AN: 5184

South Asian (SAS) AF: 0.560 AC: 2696 AN: 4818

European-Finnish (FIN) AF: 0.413 AC: 4366 AN: 10582

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.506 AC: 34371 AN: 67978

Other (OTH) AF: 0.576 AC: 1218 AN: 2116

Alfa AF: 0.544 Hom.: 3252

Bravo AF: 0.571

Asia WGS AF: 0.531 AC: 1847 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.5
DANN	Benign	0.60
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs30329; hg19: chr5-148167834;