rs558370

Variant names:

• chr1-109528491-A-G
• rs558370

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 0.586 in 151,946 control chromosomes in the GnomAD database, including 27,979 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 0.59 (27979 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.512

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.823 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: 0.586 AC: 88920 AN: 151828 Hom.: 27936 Cov.: 31

Gnomad AFR AF: 0.830

Gnomad AMI AF: 0.691

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.510

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.586 AC: 89008 AN: 151946 Hom.: 27979 Cov.: 31 AF XY: 0.580 AC XY: 43083 AN XY: 74232

Gnomad4 AFR AF: 0.831

Gnomad4 AMR AF: 0.433

Gnomad4 ASJ AF: 0.478

Gnomad4 EAS AF: 0.353

Gnomad4 SAS AF: 0.599

Gnomad4 FIN AF: 0.480

Gnomad4 NFE AF: 0.510

Gnomad4 OTH AF: 0.540

Alfa AF: 0.550 Hom.: 4059

Bravo AF: 0.588

Asia WGS AF: 0.514 AC: 1789 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.0
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: rs558370; hg19: chr1-110071113;