chr1-229587269-G-A

Variant names:

• chr1-229587269-G-A
• rs348334

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 0.826 in 134,694 control chromosomes in the GnomAD database, including 46,823 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 0.83 (46823 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.434
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.891 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: 0.826 AC: 111203 AN: 134608 Hom.: 46811 Cov.: 29

Gnomad AFR AF: 0.746

Gnomad AMI AF: 0.931

Gnomad AMR AF: 0.740

Gnomad ASJ AF: 0.849

Gnomad EAS AF: 0.601

Gnomad SAS AF: 0.868

Gnomad FIN AF: 0.897

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.897

Gnomad OTH AF: 0.823

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

GnomAD4 genome AF: 0.826 AC: 111251 AN: 134694 Hom.: 46823 Cov.: 29 AF XY: 0.823 AC XY: 53890 AN XY: 65476

African (AFR) AF: 0.746 AC: 28109 AN: 37698

American (AMR) AF: 0.740 AC: 9913 AN: 13402

Ashkenazi Jewish (ASJ) AF: 0.849 AC: 2501 AN: 2946

East Asian (EAS) AF: 0.600 AC: 2716 AN: 4528

South Asian (SAS) AF: 0.868 AC: 3690 AN: 4252

European-Finnish (FIN) AF: 0.897 AC: 8242 AN: 9192

Middle Eastern (MID) AF: 0.786 AC: 198 AN: 252

European-Non Finnish (NFE) AF: 0.897 AC: 53593 AN: 59754

Other (OTH) AF: 0.823 AC: 1503 AN: 1826

Alfa AF: 0.859 Hom.: 97591

Bravo AF: 0.804

Asia WGS AF: 0.641 AC: 1535 AN: 2388

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.1
DANN	Benign	0.30
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs348334; hg19: chr1-229723016;