chr1-46429969-A-G

Variant names:

• chr1-46429969-A-G
• rs1571138

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 0.736 in 152,182 control chromosomes in the GnomAD database, including 41,669 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 0.74 (41669 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.594
• Publications: 22 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.803 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: 0.736 AC: 111888 AN: 152064 Hom.: 41644 Cov.: 33

Gnomad AFR AF: 0.632

Gnomad AMI AF: 0.832

Gnomad AMR AF: 0.697

Gnomad ASJ AF: 0.851

Gnomad EAS AF: 0.824

Gnomad SAS AF: 0.739

Gnomad FIN AF: 0.723

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.794

Gnomad OTH AF: 0.762

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

GnomAD4 genome AF: 0.736 AC: 111962 AN: 152182 Hom.: 41669 Cov.: 33 AF XY: 0.734 AC XY: 54610 AN XY: 74412

African (AFR) AF: 0.633 AC: 26271 AN: 41504

American (AMR) AF: 0.697 AC: 10651 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.851 AC: 2954 AN: 3470

East Asian (EAS) AF: 0.824 AC: 4276 AN: 5190

South Asian (SAS) AF: 0.738 AC: 3561 AN: 4822

European-Finnish (FIN) AF: 0.723 AC: 7655 AN: 10584

Middle Eastern (MID) AF: 0.847 AC: 249 AN: 294

European-Non Finnish (NFE) AF: 0.794 AC: 53980 AN: 68002

Other (OTH) AF: 0.760 AC: 1608 AN: 2116

Alfa AF: 0.777 Hom.: 79239

Bravo AF: 0.730

Asia WGS AF: 0.786 AC: 2733 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.6
DANN	Benign	0.34
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs1571138; hg19: chr1-46895641;