14-59376688-A-G

Variant names:

• chr14-59376688-A-G
• rs1253192

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 0.92 in 152,250 control chromosomes in the GnomAD database, including 64,470 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 0.92 (64470 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.213
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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: 0.920 AC: 139964 AN: 152132 Hom.: 64420 Cov.: 31

Gnomad AFR AF: 0.899

Gnomad AMI AF: 0.859

Gnomad AMR AF: 0.916

Gnomad ASJ AF: 0.909

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.945

Gnomad FIN AF: 0.953

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.923

Gnomad OTH AF: 0.894

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

GnomAD4 genome AF: 0.920 AC: 140072 AN: 152250 Hom.: 64470 Cov.: 31 AF XY: 0.922 AC XY: 68635 AN XY: 74434

African (AFR) AF: 0.899 AC: 37329 AN: 41514

American (AMR) AF: 0.916 AC: 14016 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.909 AC: 3153 AN: 3470

East Asian (EAS) AF: 0.998 AC: 5165 AN: 5174

South Asian (SAS) AF: 0.945 AC: 4564 AN: 4830

European-Finnish (FIN) AF: 0.953 AC: 10114 AN: 10618

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.923 AC: 62817 AN: 68026

Other (OTH) AF: 0.896 AC: 1895 AN: 2114

Alfa AF: 0.922 Hom.: 12379

Bravo AF: 0.918

Asia WGS AF: 0.969 AC: 3371 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.0
DANN	Benign	0.69
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs1253192; hg19: chr14-59843406;