rs1409423

chr1-100770285-A-G

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 0.502 in 152,016 control chromosomes in the GnomAD database, including 19,691 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 0.50 (19691 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.615

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.592 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: 0.502 AC: 76235 AN: 151898 Hom.: 19674 Cov.: 32

Gnomad AFR AF: 0.598

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.367

Gnomad EAS AF: 0.609

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.505

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.490

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

GnomAD4 genome AF: 0.502 AC: 76303 AN: 152016 Hom.: 19691 Cov.: 32 AF XY: 0.505 AC XY: 37514 AN XY: 74302

Gnomad4 AFR AF: 0.598

Gnomad4 AMR AF: 0.534

Gnomad4 ASJ AF: 0.367

Gnomad4 EAS AF: 0.609

Gnomad4 SAS AF: 0.500

Gnomad4 FIN AF: 0.505

Gnomad4 NFE AF: 0.438

Gnomad4 OTH AF: 0.490

Alfa AF: 0.492 Hom.: 3186

Bravo AF: 0.510

Asia WGS AF: 0.558 AC: 1944 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.76
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1409423; hg19: chr1-101235841; COSMIC: COSV59978388;