1-228969398-A-G

Variant names:

• chr1-228969398-A-G
• rs603404

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 0.645 in 151,762 control chromosomes in the GnomAD database, including 32,012 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 0.65 (32012 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.740

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.689 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: 0.646 AC: 97895 AN: 151644 Hom.: 31994 Cov.: 30

Gnomad AFR AF: 0.596

Gnomad AMI AF: 0.812

Gnomad AMR AF: 0.644

Gnomad ASJ AF: 0.663

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.667

Gnomad MID AF: 0.650

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.643

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

GnomAD4 genome AF: 0.645 AC: 97957 AN: 151762 Hom.: 32012 Cov.: 30 AF XY: 0.642 AC XY: 47563 AN XY: 74128

Gnomad4 AFR AF: 0.595

Gnomad4 AMR AF: 0.643

Gnomad4 ASJ AF: 0.663

Gnomad4 EAS AF: 0.403

Gnomad4 SAS AF: 0.564

Gnomad4 FIN AF: 0.667

Gnomad4 NFE AF: 0.694

Gnomad4 OTH AF: 0.644

Alfa AF: 0.677 Hom.: 51728

Bravo AF: 0.642

Asia WGS AF: 0.487 AC: 1694 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	0.17
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs603404; hg19: chr1-229105145;