14-76525821-C-T

Variant names:

• chr14-76525821-C-T
• rs1676303
• ENST00000554926.1:n.311-23561G>A

Variant summary

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

The ENST00000554926.1(ENSG00000259124):​n.311-23561G>A variant causes a intron 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: ENSG00000259124 ENST00000554926.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.493
• Publications: 20 publications found

Genes affected

ENSG00000259124 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259124	ENST00000554926.1	n.311-23561G>A		intron_variant	Intron 2 of 3	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

African (AFR) AF: 0.592 AC: 24549 AN: 41450

American (AMR) AF: 0.886 AC: 13557 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.830 AC: 2880 AN: 3470

East Asian (EAS) AF: 0.822 AC: 4237 AN: 5156

South Asian (SAS) AF: 0.897 AC: 4330 AN: 4826

European-Finnish (FIN) AF: 0.865 AC: 9157 AN: 10586

Middle Eastern (MID) AF: 0.871 AC: 256 AN: 294

European-Non Finnish (NFE) AF: 0.884 AC: 60090 AN: 68002

Other (OTH) AF: 0.811 AC: 1706 AN: 2104

Alfa AF: 0.862 Hom.: 115305

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
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs1676303; hg19: chr14-76992164;