rs657420

Variant names:

• chr1-109283514-C-T
• rs657420

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 0.433 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
• Publications: 23 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.216 AC: 8973 AN: 41520

American (AMR) AF: 0.539 AC: 8238 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.505 AC: 1753 AN: 3468

East Asian (EAS) AF: 0.493 AC: 2550 AN: 5168

South Asian (SAS) AF: 0.479 AC: 2312 AN: 4824

European-Finnish (FIN) AF: 0.460 AC: 4867 AN: 10580

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.525 AC: 35698 AN: 67992

Other (OTH) AF: 0.478 AC: 1008 AN: 2110

Alfa AF: 0.488 Hom.: 11364

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
PhyloP100		-0.23
PromoterAI		-0.12	Neutral

Splicing

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

Other links and lift over

dbSNP: rs657420; hg19: chr1-109826136;