chr14-28330663-A-G

Position:

• chr14-28330663-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000548280.1(ENSG00000257869):​n.392+12131A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 152,288 control chromosomes in the GnomAD database, including 919 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 0.11 (919 hom., cov: 32)
• Consequence: ENST00000548280.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.456

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.123 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
	ENST00000548280.1	n.392+12131A>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16590 AN: 152170 Hom.: 919 Cov.: 32

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.0943

Gnomad AMR AF: 0.0727

Gnomad ASJ AF: 0.0700

Gnomad EAS AF: 0.0225

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.0844

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.0946

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

GnomAD4 genome AF: 0.109 AC: 16594 AN: 152288 Hom.: 919 Cov.: 32 AF XY: 0.106 AC XY: 7889 AN XY: 74452

Gnomad4 AFR AF: 0.116

Gnomad4 AMR AF: 0.0725

Gnomad4 ASJ AF: 0.0700

Gnomad4 EAS AF: 0.0226

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.0844

Gnomad4 NFE AF: 0.126

Gnomad4 OTH AF: 0.0937

Alfa AF: 0.116 Hom.: 459

Bravo AF: 0.108

Asia WGS AF: 0.0870 AC: 304 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.9
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7157863; hg19: chr14-28799869;