14-76525821-C-T

Position:

• chr14-76525821-C-T

Variant summary

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

The ENST00000554926.1(ENSG00000259124):​n.311-23561G>A 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 0.799 in 152,098 control chromosomes in the GnomAD database, including 49,895 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 0.80 (49895 hom., cov: 31)
• Consequence: ENST00000554926.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.493

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.878 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
	ENST00000554926.1	n.311-23561G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.800 AC: 121538 AN: 151980 Hom.: 49878 Cov.: 31

Gnomad AFR AF: 0.593

Gnomad AMI AF: 0.916

Gnomad AMR AF: 0.886

Gnomad ASJ AF: 0.830

Gnomad EAS AF: 0.822

Gnomad SAS AF: 0.898

Gnomad FIN AF: 0.865

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.884

Gnomad OTH AF: 0.811

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

GnomAD4 genome AF: 0.799 AC: 121597 AN: 152098 Hom.: 49895 Cov.: 31 AF XY: 0.802 AC XY: 59640 AN XY: 74330

Gnomad4 AFR AF: 0.592

Gnomad4 AMR AF: 0.886

Gnomad4 ASJ AF: 0.830

Gnomad4 EAS AF: 0.822

Gnomad4 SAS AF: 0.897

Gnomad4 FIN AF: 0.865

Gnomad4 NFE AF: 0.884

Gnomad4 OTH AF: 0.811

Alfa AF: 0.868 Hom.: 84994

Bravo AF: 0.791

Asia WGS AF: 0.831 AC: 2891 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.1
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1676303; hg19: chr14-76992164;