rs657420

chr1-109283514-C-T

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 0.433 in 152,160 control chromosomes in the GnomAD database, including 15,907 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 0.43 (15907 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.230

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.529 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: 0.433 AC: 65863 AN: 152042 Hom.: 15899 Cov.: 33

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.493

Gnomad SAS AF: 0.479

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.474

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

GnomAD4 genome AF: 0.433 AC: 65884 AN: 152160 Hom.: 15907 Cov.: 33 AF XY: 0.431 AC XY: 32036 AN XY: 74384

Gnomad4 AFR AF: 0.216

Gnomad4 AMR AF: 0.539

Gnomad4 ASJ AF: 0.505

Gnomad4 EAS AF: 0.493

Gnomad4 SAS AF: 0.479

Gnomad4 FIN AF: 0.460

Gnomad4 NFE AF: 0.525

Gnomad4 OTH AF: 0.478

Alfa AF: 0.492 Hom.: 9879

Bravo AF: 0.429

Asia WGS AF: 0.478 AC: 1660 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
Cadd	Benign	3.4
Dann	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs657420; hg19: chr1-109826136;