1-28886822-C-A

Variant names:

• chr1-28886822-C-A
• rs157224

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.125 AC: 5203 AN: 41468

American (AMR) AF: 0.0819 AC: 1252 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0875 AC: 303 AN: 3464

East Asian (EAS) AF: 0.126 AC: 654 AN: 5172

South Asian (SAS) AF: 0.144 AC: 695 AN: 4828

European-Finnish (FIN) AF: 0.0928 AC: 983 AN: 10592

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0704 AC: 4790 AN: 67992

Other (OTH) AF: 0.0979 AC: 207 AN: 2114

Alfa AF: 0.0760 Hom.: 646

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
PhyloP100		1.1
PromoterAI		-0.088	Neutral

Splicing

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

Other links and lift over

dbSNP: rs157224; hg19: chr1-29213334;