rs430952

Variant names:

• chr5-117642122-G-A
• rs430952

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 0.408 in 151,982 control chromosomes in the GnomAD database, including 14,435 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 0.41 (14435 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.627 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: 0.408 AC: 61890 AN: 151864 Hom.: 14428 Cov.: 32

Gnomad AFR AF: 0.634

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.0412

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.414

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

GnomAD4 genome AF: 0.408 AC: 61933 AN: 151982 Hom.: 14435 Cov.: 32 AF XY: 0.403 AC XY: 29930 AN XY: 74274

Gnomad4 AFR AF: 0.634

Gnomad4 AMR AF: 0.292

Gnomad4 ASJ AF: 0.357

Gnomad4 EAS AF: 0.0411

Gnomad4 SAS AF: 0.299

Gnomad4 FIN AF: 0.318

Gnomad4 NFE AF: 0.347

Gnomad4 OTH AF: 0.411

Alfa AF: 0.410 Hom.: 1786

Bravo AF: 0.411

Asia WGS AF: 0.213 AC: 741 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.41
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs430952; hg19: chr5-116977817;