rs127557

Variant names:

• chr1-228792151-G-A
• rs127557

Your query was ambiguous. Multiple possible variants found:

• chr1-228792151-G-A
• chr1-228792151-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;