14-103146855-A-C

Variant names:

• chr14-103146855-A-C
• rs719252

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 0.807 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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

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: 0.807 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

African (AFR) AF: 0.861 AC: 35769 AN: 41532

American (AMR) AF: 0.790 AC: 12075 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.888 AC: 3082 AN: 3470

East Asian (EAS) AF: 0.748 AC: 3864 AN: 5166

South Asian (SAS) AF: 0.707 AC: 3402 AN: 4814

European-Finnish (FIN) AF: 0.681 AC: 7187 AN: 10558

Middle Eastern (MID) AF: 0.823 AC: 242 AN: 294

European-Non Finnish (NFE) AF: 0.803 AC: 54579 AN: 67990

Other (OTH) AF: 0.830 AC: 1753 AN: 2112

Alfa AF: 0.793 Hom.: 22070

Bravo AF: 0.822

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.31
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs719252; hg19: chr14-103613192;