rs2178490

Variant names:

• chr5-30839224-A-G
• rs2178490

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 0.285 in 151,942 control chromosomes in the GnomAD database, including 7,117 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 0.28 (7117 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.96

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.653 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: 0.285 AC: 43227 AN: 151824 Hom.: 7089 Cov.: 32

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.672

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.285 AC: 43294 AN: 151942 Hom.: 7117 Cov.: 32 AF XY: 0.287 AC XY: 21336 AN XY: 74254

Gnomad4 AFR AF: 0.372

Gnomad4 AMR AF: 0.327

Gnomad4 ASJ AF: 0.243

Gnomad4 EAS AF: 0.672

Gnomad4 SAS AF: 0.394

Gnomad4 FIN AF: 0.168

Gnomad4 NFE AF: 0.207

Gnomad4 OTH AF: 0.286

Alfa AF: 0.235 Hom.: 7615

Bravo AF: 0.303

Asia WGS AF: 0.545 AC: 1893 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.0010
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2178490; hg19: chr5-30839331;