ENST00000555328.1:n.500+2939C>T

Variant names:

• chr14-101260770-C-T
• rs2400997
• ENST00000555328.1:n.500+2939C>T

Variant summary

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

The ENST00000555328.1(ENSG00000258497):​n.500+2939C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.429 in 151,982 control chromosomes in the GnomAD database, including 14,387 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 0.43 (14387 hom., cov: 32)
• Consequence: ENSG00000258497 ENST00000555328.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79

Genes affected

ENSG00000258497 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.473 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
ENSG00000258497	ENST00000555328.1	n.500+2939C>T		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.429 AC: 65200 AN: 151864 Hom.: 14384 Cov.: 32

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.454

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

GnomAD4 genome AF: 0.429 AC: 65245 AN: 151982 Hom.: 14387 Cov.: 32 AF XY: 0.425 AC XY: 31592 AN XY: 74282

Gnomad4 AFR AF: 0.369

Gnomad4 AMR AF: 0.479

Gnomad4 ASJ AF: 0.507

Gnomad4 EAS AF: 0.191

Gnomad4 SAS AF: 0.400

Gnomad4 FIN AF: 0.377

Gnomad4 NFE AF: 0.477

Gnomad4 OTH AF: 0.451

Alfa AF: 0.468 Hom.: 36704

Bravo AF: 0.430

Asia WGS AF: 0.295 AC: 1028 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.82
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2400997; hg19: chr14-101727107;