5-148783761-A-G

Variant names:

• chr5-148783761-A-G
• rs30325

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 0.468 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
• Publications: 5 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 (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

African (AFR) AF: 0.469 AC: 19448 AN: 41426

American (AMR) AF: 0.500 AC: 7641 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.549 AC: 1905 AN: 3468

East Asian (EAS) AF: 0.333 AC: 1723 AN: 5168

South Asian (SAS) AF: 0.500 AC: 2405 AN: 4810

European-Finnish (FIN) AF: 0.396 AC: 4194 AN: 10592

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.475 AC: 32269 AN: 67972

Other (OTH) AF: 0.496 AC: 1043 AN: 2102

Alfa AF: 0.473 Hom.: 32023

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
PhyloP100		0.035

Splicing

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

Other links and lift over

dbSNP: rs30325; hg19: chr5-148163324;