rs8019172

chr14-52179201-A-Cchr14-52179201-A-Gchr14-52179201-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 0.868 in 152,184 control chromosomes in the GnomAD database, including 57,658 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 0.87 (57658 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.161

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.914 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.868 AC: 131938 AN: 152066 Hom.: 57623 Cov.: 32

Gnomad AFR AF: 0.761

Gnomad AMI AF: 0.758

Gnomad AMR AF: 0.910

Gnomad ASJ AF: 0.906

Gnomad EAS AF: 0.901

Gnomad SAS AF: 0.938

Gnomad FIN AF: 0.931

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.904

Gnomad OTH AF: 0.877

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

GnomAD4 genome AF: 0.868 AC: 132029 AN: 152184 Hom.: 57658 Cov.: 32 AF XY: 0.871 AC XY: 64812 AN XY: 74402

Gnomad4 AFR AF: 0.762

Gnomad4 AMR AF: 0.910

Gnomad4 ASJ AF: 0.906

Gnomad4 EAS AF: 0.901

Gnomad4 SAS AF: 0.937

Gnomad4 FIN AF: 0.931

Gnomad4 NFE AF: 0.904

Gnomad4 OTH AF: 0.878

Alfa AF: 0.893 Hom.: 27661

Bravo AF: 0.861

Asia WGS AF: 0.920 AC: 3200 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	3.8
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8019172; hg19: chr14-52645919;