rs28788874

Variant names:

• chr1-1585345-C-T
• rs28788874

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 0.303 in 151,772 control chromosomes in the GnomAD database, including 8,249 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 0.30 (8249 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.70

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.406 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: 0.303 AC: 45989 AN: 151654 Hom.: 8249 Cov.: 32

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.347

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

GnomAD4 genome AF: 0.303 AC: 45983 AN: 151772 Hom.: 8249 Cov.: 32 AF XY: 0.299 AC XY: 22163 AN XY: 74150

Gnomad4 AFR AF: 0.126

Gnomad4 AMR AF: 0.270

Gnomad4 ASJ AF: 0.480

Gnomad4 EAS AF: 0.143

Gnomad4 SAS AF: 0.250

Gnomad4 FIN AF: 0.373

Gnomad4 NFE AF: 0.410

Gnomad4 OTH AF: 0.345

Alfa AF: 0.334 Hom.: 1189

Bravo AF: 0.287

Asia WGS AF: 0.203 AC: 707 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.24
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs28788874; hg19: chr1-1520725;