rs30325

Variant names:

• chr5-148783761-A-G
• rs30325

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.468 in 152,022 control chromosomes in the GnomAD database, including 16,933 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 0.47 (16933 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0350

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.491 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: 0.468 AC: 71144 AN: 151904 Hom.: 16919 Cov.: 32

Gnomad AFR AF: 0.470

Gnomad AMI AF: 0.420

Gnomad AMR AF: 0.500

Gnomad ASJ AF: 0.549

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.499

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.495

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

GnomAD4 genome AF: 0.468 AC: 71196 AN: 152022 Hom.: 16933 Cov.: 32 AF XY: 0.467 AC XY: 34680 AN XY: 74312

Gnomad4 AFR AF: 0.469

Gnomad4 AMR AF: 0.500

Gnomad4 ASJ AF: 0.549

Gnomad4 EAS AF: 0.333

Gnomad4 SAS AF: 0.500

Gnomad4 FIN AF: 0.396

Gnomad4 NFE AF: 0.475

Gnomad4 OTH AF: 0.496

Alfa AF: 0.474 Hom.: 8633

Bravo AF: 0.474

Asia WGS AF: 0.443 AC: 1541 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	4.5
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs30325; hg19: chr5-148163324;