14-82563201-A-G

Variant names:

• chr14-82563201-A-G
• rs2372200

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 0.736 in 152,042 control chromosomes in the GnomAD database, including 41,688 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 0.74 (41688 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.163
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.807 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: 0.736 AC: 111858 AN: 151924 Hom.: 41665 Cov.: 32

Gnomad AFR AF: 0.629

Gnomad AMI AF: 0.775

Gnomad AMR AF: 0.697

Gnomad ASJ AF: 0.788

Gnomad EAS AF: 0.754

Gnomad SAS AF: 0.828

Gnomad FIN AF: 0.781

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.791

Gnomad OTH AF: 0.757

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

GnomAD4 genome AF: 0.736 AC: 111925 AN: 152042 Hom.: 41688 Cov.: 32 AF XY: 0.737 AC XY: 54777 AN XY: 74316

African (AFR) AF: 0.629 AC: 26083 AN: 41486

American (AMR) AF: 0.698 AC: 10648 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.788 AC: 2733 AN: 3468

East Asian (EAS) AF: 0.754 AC: 3871 AN: 5134

South Asian (SAS) AF: 0.828 AC: 3991 AN: 4820

European-Finnish (FIN) AF: 0.781 AC: 8259 AN: 10578

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.791 AC: 53802 AN: 67982

Other (OTH) AF: 0.759 AC: 1601 AN: 2110

Alfa AF: 0.781 Hom.: 33820

Bravo AF: 0.724

Asia WGS AF: 0.780 AC: 2711 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.57
DANN	Benign	0.48
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs2372200; hg19: chr14-83029545;