rs30306

Variant names:

• chr5-148772801-A-G
• rs30306

Your query was ambiguous. Multiple possible variants found:

• chr5-148772801-A-G
• chr5-148772801-A-T

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 0.538 in 152,002 control chromosomes in the GnomAD database, including 22,570 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 0.54 (22570 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.545
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.63 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: 0.538 AC: 81762 AN: 151882 Hom.: 22539 Cov.: 32

Gnomad AFR AF: 0.637

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.538

Gnomad ASJ AF: 0.599

Gnomad EAS AF: 0.386

Gnomad SAS AF: 0.560

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.556

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

GnomAD4 genome AF: 0.538 AC: 81833 AN: 152002 Hom.: 22570 Cov.: 32 AF XY: 0.534 AC XY: 39663 AN XY: 74298

African (AFR) AF: 0.637 AC: 26387 AN: 41442

American (AMR) AF: 0.538 AC: 8223 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.599 AC: 2078 AN: 3468

East Asian (EAS) AF: 0.387 AC: 1994 AN: 5156

South Asian (SAS) AF: 0.561 AC: 2707 AN: 4822

European-Finnish (FIN) AF: 0.413 AC: 4365 AN: 10558

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.505 AC: 34319 AN: 67970

Other (OTH) AF: 0.555 AC: 1172 AN: 2112

Alfa AF: 0.512 Hom.: 10127

Bravo AF: 0.548

Asia WGS AF: 0.518 AC: 1803 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.66
DANN	Benign	0.35
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs30306; hg19: chr5-148152364;