14-94895874-C-G

Position:

• chr14-94895874-C-G

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 0.163 in 152,184 control chromosomes in the GnomAD database, including 2,877 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 0.16 (2877 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.189

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 = 0.543 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: 0.163 AC: 24759 AN: 152068 Hom.: 2885 Cov.: 33

Gnomad AFR AF: 0.0560

Gnomad AMI AF: 0.0714

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.561

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.163 AC: 24749 AN: 152184 Hom.: 2877 Cov.: 33 AF XY: 0.167 AC XY: 12413 AN XY: 74406

Gnomad4 AFR AF: 0.0560

Gnomad4 AMR AF: 0.222

Gnomad4 ASJ AF: 0.151

Gnomad4 EAS AF: 0.560

Gnomad4 SAS AF: 0.367

Gnomad4 FIN AF: 0.136

Gnomad4 NFE AF: 0.176

Gnomad4 OTH AF: 0.170

Alfa AF: 0.0612 Hom.: 78

Bravo AF: 0.165

Asia WGS AF: 0.380 AC: 1319 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	2.5
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10484048; hg19: chr14-95362211;