rs1426562

Variant names:

• chr8-53023134-A-G
• rs1426562

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 0.349 in 152,062 control chromosomes in the GnomAD database, including 13,607 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 0.35 (13607 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.17
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.723 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52945 AN: 151944 Hom.: 13583 Cov.: 32

Gnomad AFR AF: 0.731

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.349 AC: 53026 AN: 152062 Hom.: 13607 Cov.: 32 AF XY: 0.344 AC XY: 25597 AN XY: 74340

African (AFR) AF: 0.730 AC: 30263 AN: 41436

American (AMR) AF: 0.213 AC: 3261 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.238 AC: 824 AN: 3464

East Asian (EAS) AF: 0.185 AC: 955 AN: 5172

South Asian (SAS) AF: 0.303 AC: 1462 AN: 4824

European-Finnish (FIN) AF: 0.192 AC: 2027 AN: 10578

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.195 AC: 13273 AN: 67990

Other (OTH) AF: 0.310 AC: 653 AN: 2104

Alfa AF: 0.223 Hom.: 5724

Bravo AF: 0.362

Asia WGS AF: 0.288 AC: 1003 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.9
DANN	Benign	0.85
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs1426562; hg19: chr8-53935694;