rs2383529

Variant names:

• chr1-186699960-A-G
• rs2383529

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.31 in 152,072 control chromosomes in the GnomAD database, including 9,332 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 0.31 (9332 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.298
• Publications: 13 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.561 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: 0.309 AC: 46958 AN: 151952 Hom.: 9284 Cov.: 32

Gnomad AFR AF: 0.567

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.0500

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.310 AC: 47067 AN: 152072 Hom.: 9332 Cov.: 32 AF XY: 0.302 AC XY: 22468 AN XY: 74366

African (AFR) AF: 0.567 AC: 23537 AN: 41476

American (AMR) AF: 0.222 AC: 3392 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.252 AC: 872 AN: 3464

East Asian (EAS) AF: 0.0498 AC: 258 AN: 5184

South Asian (SAS) AF: 0.261 AC: 1259 AN: 4820

European-Finnish (FIN) AF: 0.169 AC: 1791 AN: 10568

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.222 AC: 15084 AN: 67966

Other (OTH) AF: 0.297 AC: 628 AN: 2116

Alfa AF: 0.244 Hom.: 7782

Bravo AF: 0.323

Asia WGS AF: 0.213 AC: 741 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	1.8
DANN	Benign	0.55
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs2383529; hg19: chr1-186669092;