rs1253192

Positions:

• chr14-59376688-A-G
• chr14-59376688-A-T

Variant summary

Our verdict is Benign. Variant got -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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.213

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.59376688A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.899

Gnomad4 AMR AF: 0.916

Gnomad4 ASJ AF: 0.909

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.945

Gnomad4 FIN AF: 0.953

Gnomad4 NFE AF: 0.923

Gnomad4 OTH AF: 0.896

Alfa AF: 0.923 Hom.: 12073

Bravo AF: 0.918

Asia WGS AF: 0.969 AC: 3371 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1253192; hg19: chr14-59843406;