14-20766609-C-G

Variant names:

• chr14-20766609-C-G
• rs762038
• ENST00000796740.1:n.79-3766G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000796740.1(ENSG00000303727):​n.79-3766G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000303727 ENST00000796740.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.300
• Publications: 2 publications found

Genes affected

ENSG00000303727 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC107984671	XR_001750622.2	n.627-3766G>C		intron_variant	Intron 1 of 2
LOC107984671	XR_001750623.2	n.627-3766G>C		intron_variant	Intron 1 of 3
LOC107984671	XR_001750624.2	n.627-3766G>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303727	ENST00000796740.1	n.79-3766G>C		intron_variant	Intron 1 of 2
ENSG00000303727	ENST00000796741.1	n.72-3766G>C		intron_variant	Intron 1 of 2
ENSG00000303727	ENST00000796742.1	n.65-3766G>C		intron_variant	Intron 1 of 3

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

African (AFR) AF: 0.807 AC: 33502 AN: 41522

American (AMR) AF: 0.704 AC: 10776 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.792 AC: 2751 AN: 3472

East Asian (EAS) AF: 0.967 AC: 5023 AN: 5192

South Asian (SAS) AF: 0.816 AC: 3943 AN: 4830

European-Finnish (FIN) AF: 0.854 AC: 9061 AN: 10604

Middle Eastern (MID) AF: 0.866 AC: 253 AN: 292

European-Non Finnish (NFE) AF: 0.769 AC: 52310 AN: 67998

Other (OTH) AF: 0.779 AC: 1647 AN: 2114

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
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs762038; hg19: chr14-21234768;