rs30325

chr5-148783761-A-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;