rs719252

Positions:

• chr14-103146855-A-C
• chr14-103146855-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 0.807 in 152,136 control chromosomes in the GnomAD database, including 49,748 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 0.81 (49748 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.122

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.854 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.807 AC: 122660 AN: 152018 Hom.: 49731 Cov.: 33

Gnomad AFR AF: 0.862

Gnomad AMI AF: 0.859

Gnomad AMR AF: 0.790

Gnomad ASJ AF: 0.888

Gnomad EAS AF: 0.748

Gnomad SAS AF: 0.707

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.803

Gnomad OTH AF: 0.829

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

GnomAD4 genome AF: 0.807 AC: 122736 AN: 152136 Hom.: 49748 Cov.: 33 AF XY: 0.798 AC XY: 59343 AN XY: 74368

Gnomad4 AFR AF: 0.861

Gnomad4 AMR AF: 0.790

Gnomad4 ASJ AF: 0.888

Gnomad4 EAS AF: 0.748

Gnomad4 SAS AF: 0.707

Gnomad4 FIN AF: 0.681

Gnomad4 NFE AF: 0.803

Gnomad4 OTH AF: 0.830

Alfa AF: 0.790 Hom.: 19211

Bravo AF: 0.822

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs719252; hg19: chr14-103613192;