rs1432265

Variant names:

• chr2-85113243-A-G
• rs1432265

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 0.322 in 152,148 control chromosomes in the GnomAD database, including 8,227 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 0.32 (8227 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.831
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.355 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.322 AC: 49029 AN: 152030 Hom.: 8220 Cov.: 33

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.504

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.322 AC: 49067 AN: 152148 Hom.: 8227 Cov.: 33 AF XY: 0.319 AC XY: 23730 AN XY: 74390

African (AFR) AF: 0.360 AC: 14944 AN: 41512

American (AMR) AF: 0.198 AC: 3026 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.336 AC: 1165 AN: 3472

East Asian (EAS) AF: 0.140 AC: 726 AN: 5174

South Asian (SAS) AF: 0.246 AC: 1188 AN: 4822

European-Finnish (FIN) AF: 0.373 AC: 3949 AN: 10582

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.336 AC: 22868 AN: 67988

Other (OTH) AF: 0.304 AC: 641 AN: 2112

Alfa AF: 0.324 Hom.: 23856

Bravo AF: 0.310

Asia WGS AF: 0.204 AC: 709 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.9
DANN	Benign	0.71
PhyloP100		0.83

Splicing

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

Other links and lift over

dbSNP: rs1432265; hg19: chr2-85340366;