ENST00000550089.2:n.463+3754G>C

Variant names:

• chr14-36002338-G-C
• rs847501
• ENST00000550089.2:n.463+3754G>C

Variant summary

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

The ENST00000550089.2(ENSG00000258342):​n.463+3754G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.517 in 151,900 control chromosomes in the GnomAD database, including 24,150 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 0.52 (24150 hom., cov: 30)
• Consequence: ENSG00000258342 ENST00000550089.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00200

Genes affected

ENSG00000258342 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.849 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
ENSG00000258342	ENST00000550089.2	n.463+3754G>C		intron_variant	Intron 3 of 4	3
ENSG00000258342	ENST00000660969.2	n.515+3754G>C		intron_variant	Intron 3 of 3
ENSG00000258342	ENST00000662718.1	n.256+3754G>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.516 AC: 78389 AN: 151782 Hom.: 24100 Cov.: 30

Gnomad AFR AF: 0.856

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.401

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.737

Gnomad SAS AF: 0.543

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.358

Gnomad OTH AF: 0.446

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

GnomAD4 genome AF: 0.517 AC: 78496 AN: 151900 Hom.: 24150 Cov.: 30 AF XY: 0.514 AC XY: 38135 AN XY: 74246

Gnomad4 AFR AF: 0.857

Gnomad4 AMR AF: 0.401

Gnomad4 ASJ AF: 0.380

Gnomad4 EAS AF: 0.737

Gnomad4 SAS AF: 0.543

Gnomad4 FIN AF: 0.315

Gnomad4 NFE AF: 0.358

Gnomad4 OTH AF: 0.444

Alfa AF: 0.443 Hom.: 2138

Bravo AF: 0.538

Asia WGS AF: 0.654 AC: 2275 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.6
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs847501; hg19: chr14-36471544;