rs429201

chr1-158225109-C-T

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 0.613 in 152,030 control chromosomes in the GnomAD database, including 32,590 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 0.61 (32590 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.98

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.783 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.614 AC: 93203 AN: 151912 Hom.: 32588 Cov.: 32

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.871

Gnomad AMR AF: 0.675

Gnomad ASJ AF: 0.751

Gnomad EAS AF: 0.514

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.755

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.788

Gnomad OTH AF: 0.669

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

GnomAD4 genome AF: 0.613 AC: 93212 AN: 152030 Hom.: 32590 Cov.: 32 AF XY: 0.611 AC XY: 45401 AN XY: 74326

Gnomad4 AFR AF: 0.265

Gnomad4 AMR AF: 0.675

Gnomad4 ASJ AF: 0.751

Gnomad4 EAS AF: 0.514

Gnomad4 SAS AF: 0.549

Gnomad4 FIN AF: 0.755

Gnomad4 NFE AF: 0.788

Gnomad4 OTH AF: 0.672

Alfa AF: 0.732 Hom.: 18483

Bravo AF: 0.596

Asia WGS AF: 0.557 AC: 1936 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.44
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs429201; hg19: chr1-158194899;