rs429201

Variant names:

• chr1-158225109-C-T
• rs429201

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.265 AC: 10991 AN: 41424

American (AMR) AF: 0.675 AC: 10307 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.751 AC: 2607 AN: 3472

East Asian (EAS) AF: 0.514 AC: 2651 AN: 5158

South Asian (SAS) AF: 0.549 AC: 2644 AN: 4814

European-Finnish (FIN) AF: 0.755 AC: 7988 AN: 10582

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.788 AC: 53602 AN: 67990

Other (OTH) AF: 0.672 AC: 1419 AN: 2112

Alfa AF: 0.731 Hom.: 20835

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
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs429201; hg19: chr1-158194899;