chr5-30174461-A-G

Position:

• chr5-30174461-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 0.225 in 152,128 control chromosomes in the GnomAD database, including 4,796 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 0.23 (4796 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.418

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.225 AC: 34249 AN: 152010 Hom.: 4800 Cov.: 33

Gnomad AFR AF: 0.0824

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.00193

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.225 AC: 34244 AN: 152128 Hom.: 4796 Cov.: 33 AF XY: 0.222 AC XY: 16483 AN XY: 74344

Gnomad4 AFR AF: 0.0822

Gnomad4 AMR AF: 0.213

Gnomad4 ASJ AF: 0.293

Gnomad4 EAS AF: 0.00193

Gnomad4 SAS AF: 0.182

Gnomad4 FIN AF: 0.320

Gnomad4 NFE AF: 0.313

Gnomad4 OTH AF: 0.244

Alfa AF: 0.266 Hom.: 771

Bravo AF: 0.211

Asia WGS AF: 0.0950 AC: 329 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.5
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4867029; hg19: chr5-30174568;