1-242908396-G-A

Variant names:

• chr1-242908396-G-A
• rs2502349

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 0.155 in 151,596 control chromosomes in the GnomAD database, including 3,790 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 0.16 (3790 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0370
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.408 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.155 AC: 23478 AN: 151476 Hom.: 3775 Cov.: 31

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.0834

Gnomad ASJ AF: 0.0455

Gnomad EAS AF: 0.0307

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.0529

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0507

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.155 AC: 23535 AN: 151596 Hom.: 3790 Cov.: 31 AF XY: 0.153 AC XY: 11333 AN XY: 74104

African (AFR) AF: 0.413 AC: 16937 AN: 40990

American (AMR) AF: 0.0832 AC: 1269 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.0455 AC: 158 AN: 3470

East Asian (EAS) AF: 0.0308 AC: 160 AN: 5192

South Asian (SAS) AF: 0.139 AC: 670 AN: 4804

European-Finnish (FIN) AF: 0.0529 AC: 561 AN: 10598

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0506 AC: 3442 AN: 67966

Other (OTH) AF: 0.139 AC: 293 AN: 2114

Alfa AF: 0.0277 Hom.: 31

Bravo AF: 0.168

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.39
PhyloP100		0.037

Splicing

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

Other links and lift over

dbSNP: rs2502349; hg19: chr1-243071698;