5-148788769-C-T

Variant names:

• chr5-148788769-C-T
• rs30330

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 0.495 in 151,888 control chromosomes in the GnomAD database, including 19,052 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 0.50 (19052 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.231
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.562 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: 0.495 AC: 75140 AN: 151770 Hom.: 19030 Cov.: 32

Gnomad AFR AF: 0.568

Gnomad AMI AF: 0.420

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.486

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.508

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

GnomAD4 genome AF: 0.495 AC: 75209 AN: 151888 Hom.: 19052 Cov.: 32 AF XY: 0.492 AC XY: 36535 AN XY: 74244

African (AFR) AF: 0.568 AC: 23502 AN: 41396

American (AMR) AF: 0.506 AC: 7720 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.550 AC: 1908 AN: 3470

East Asian (EAS) AF: 0.318 AC: 1637 AN: 5152

South Asian (SAS) AF: 0.487 AC: 2348 AN: 4820

European-Finnish (FIN) AF: 0.394 AC: 4155 AN: 10540

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.475 AC: 32292 AN: 67948

Other (OTH) AF: 0.509 AC: 1075 AN: 2112

Alfa AF: 0.490 Hom.: 30472

Bravo AF: 0.505

Asia WGS AF: 0.431 AC: 1501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.8
DANN	Benign	0.48
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs30330; hg19: chr5-148168332;