rs2383529

chr1-186699960-A-G

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 0.31 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

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 (AFR) allele frequency at 95% confidence interval = 0.561 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: 0.309 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

Gnomad4 AFR AF: 0.567

Gnomad4 AMR AF: 0.222

Gnomad4 ASJ AF: 0.252

Gnomad4 EAS AF: 0.0498

Gnomad4 SAS AF: 0.261

Gnomad4 FIN AF: 0.169

Gnomad4 NFE AF: 0.222

Gnomad4 OTH AF: 0.297

Alfa AF: 0.242 Hom.: 6519

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2383529; hg19: chr1-186669092;