rs177216

chr14-78063343-G-Achr14-78063343-G-C

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 0.0962 in 152,258 control chromosomes in the GnomAD database, including 946 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 0.096 (946 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.335

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.171 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: 0.0962 AC: 14643 AN: 152140 Hom.: 942 Cov.: 33

Gnomad AFR AF: 0.0214

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.0565

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.0686

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

GnomAD4 genome AF: 0.0962 AC: 14646 AN: 152258 Hom.: 946 Cov.: 33 AF XY: 0.101 AC XY: 7554 AN XY: 74434

Gnomad4 AFR AF: 0.0213

Gnomad4 AMR AF: 0.157

Gnomad4 ASJ AF: 0.0565

Gnomad4 EAS AF: 0.181

Gnomad4 SAS AF: 0.175

Gnomad4 FIN AF: 0.154

Gnomad4 NFE AF: 0.108

Gnomad4 OTH AF: 0.0683

Alfa AF: 0.102 Hom.: 189

Bravo AF: 0.0912

Asia WGS AF: 0.157 AC: 545 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	3.2
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: rs177216; hg19: chr14-78529686;