rs430306

Variant names:

• chr1-112109397-G-A
• rs430306

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 0.805 in 151,892 control chromosomes in the GnomAD database, including 49,588 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 0.80 (49588 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365

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 (EAS) allele frequency at 95% confidence interval = 0.97 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: 0.805 AC: 122140 AN: 151772 Hom.: 49549 Cov.: 32

Gnomad AFR AF: 0.887

Gnomad AMI AF: 0.711

Gnomad AMR AF: 0.764

Gnomad ASJ AF: 0.734

Gnomad EAS AF: 0.992

Gnomad SAS AF: 0.831

Gnomad FIN AF: 0.753

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.762

Gnomad OTH AF: 0.775

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

GnomAD4 genome AF: 0.805 AC: 122237 AN: 151892 Hom.: 49588 Cov.: 32 AF XY: 0.805 AC XY: 59708 AN XY: 74198

Gnomad4 AFR AF: 0.886

Gnomad4 AMR AF: 0.763

Gnomad4 ASJ AF: 0.734

Gnomad4 EAS AF: 0.992

Gnomad4 SAS AF: 0.832

Gnomad4 FIN AF: 0.753

Gnomad4 NFE AF: 0.762

Gnomad4 OTH AF: 0.777

Alfa AF: 0.797 Hom.: 7642

Bravo AF: 0.805

Asia WGS AF: 0.895 AC: 3111 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.0
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs430306; hg19: chr1-112652019;