rs127557

chr1-228792151-G-Achr1-228792151-G-C

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 0.516 in 151,980 control chromosomes in the GnomAD database, including 22,048 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 0.52 (22048 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0930

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 (NFE) allele frequency at 95% confidence interval = 0.614 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: 0.516 AC: 78419 AN: 151862 Hom.: 22037 Cov.: 32

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.591

Gnomad ASJ AF: 0.548

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.700

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.619

Gnomad OTH AF: 0.541

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

GnomAD4 genome AF: 0.516 AC: 78468 AN: 151980 Hom.: 22048 Cov.: 32 AF XY: 0.521 AC XY: 38689 AN XY: 74276

Gnomad4 AFR AF: 0.274

Gnomad4 AMR AF: 0.591

Gnomad4 ASJ AF: 0.548

Gnomad4 EAS AF: 0.482

Gnomad4 SAS AF: 0.543

Gnomad4 FIN AF: 0.700

Gnomad4 NFE AF: 0.619

Gnomad4 OTH AF: 0.543

Alfa AF: 0.589 Hom.: 28466

Bravo AF: 0.494

Asia WGS AF: 0.509 AC: 1772 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.83
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs127557; hg19: chr1-228927898;