14-20766609-C-G

Position:

• chr14-20766609-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 0.788 in 152,232 control chromosomes in the GnomAD database, including 47,553 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 0.79 (47553 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.300

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.945 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.20766609C>G		intergenic_region
LOC107984671	XR_001750622.2	n.627-3766G>C		intron_variant
LOC107984671	XR_001750623.2	n.627-3766G>C		intron_variant
LOC107984671	XR_001750624.2	n.627-3766G>C		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.788 AC: 119908 AN: 152114 Hom.: 47501 Cov.: 33

Gnomad AFR AF: 0.806

Gnomad AMI AF: 0.816

Gnomad AMR AF: 0.705

Gnomad ASJ AF: 0.792

Gnomad EAS AF: 0.968

Gnomad SAS AF: 0.816

Gnomad FIN AF: 0.854

Gnomad MID AF: 0.863

Gnomad NFE AF: 0.769

Gnomad OTH AF: 0.776

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

GnomAD4 genome AF: 0.788 AC: 120010 AN: 152232 Hom.: 47553 Cov.: 33 AF XY: 0.794 AC XY: 59087 AN XY: 74434

Gnomad4 AFR AF: 0.807

Gnomad4 AMR AF: 0.704

Gnomad4 ASJ AF: 0.792

Gnomad4 EAS AF: 0.967

Gnomad4 SAS AF: 0.816

Gnomad4 FIN AF: 0.854

Gnomad4 NFE AF: 0.769

Gnomad4 OTH AF: 0.779

Alfa AF: 0.775 Hom.: 5681

Bravo AF: 0.776

Asia WGS AF: 0.902 AC: 3139 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs762038; hg19: chr14-21234768;