14-78063343-G-A

Variant names:

• chr14-78063343-G-A
• rs177216

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 0.0962 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0213 AC: 886 AN: 41562

American (AMR) AF: 0.157 AC: 2396 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0565 AC: 196 AN: 3472

East Asian (EAS) AF: 0.181 AC: 935 AN: 5178

South Asian (SAS) AF: 0.175 AC: 844 AN: 4826

European-Finnish (FIN) AF: 0.154 AC: 1629 AN: 10596

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.108 AC: 7377 AN: 68010

Other (OTH) AF: 0.0683 AC: 144 AN: 2108

Alfa AF: 0.0998 Hom.: 190

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
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs177216; hg19: chr14-78529686;