rs157224

chr1-28886822-C-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.093 in 152,128 control chromosomes in the GnomAD database, including 728 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 0.093 (728 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.42).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.135 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: 0.0930 AC: 14136 AN: 152010 Hom.: 726 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.0820

Gnomad ASJ AF: 0.0875

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.0928

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0705

Gnomad OTH AF: 0.0989

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

GnomAD4 genome AF: 0.0930 AC: 14145 AN: 152128 Hom.: 728 Cov.: 32 AF XY: 0.0953 AC XY: 7088 AN XY: 74390

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.0819

Gnomad4 ASJ AF: 0.0875

Gnomad4 EAS AF: 0.126

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.0928

Gnomad4 NFE AF: 0.0704

Gnomad4 OTH AF: 0.0979

Alfa AF: 0.0863 Hom.: 95

Bravo AF: 0.0906

Asia WGS AF: 0.154 AC: 534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
Cadd	Benign	15
Dann	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs157224; hg19: chr1-29213334;