14-101260770-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 16 publications found

Genes affected

ENSG00000258497 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.369 AC: 15294 AN: 41466

American (AMR) AF: 0.479 AC: 7313 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.507 AC: 1760 AN: 3472

East Asian (EAS) AF: 0.191 AC: 989 AN: 5184

South Asian (SAS) AF: 0.400 AC: 1920 AN: 4800

European-Finnish (FIN) AF: 0.377 AC: 3971 AN: 10542

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.477 AC: 32416 AN: 67950

Other (OTH) AF: 0.451 AC: 949 AN: 2104

Alfa AF: 0.462 Hom.: 71829

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
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs2400997; hg19: chr14-101727107;