ENST00000776599.1:n.556+2381T>C

Variant names:

• chr4-122600025-A-G
• rs975405
• ENST00000776599.1:n.556+2381T>C

Variant summary

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

The ENST00000776599.1(ENSG00000301148):​n.556+2381T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.412 in 151,782 control chromosomes in the GnomAD database, including 13,108 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 0.41 (13108 hom., cov: 31)
• Consequence: ENSG00000301148 ENST00000776599.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.507
• Publications: 7 publications found

Genes affected

ENSG00000301148 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.443 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
ENSG00000301148	ENST00000776599.1	n.556+2381T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62523 AN: 151664 Hom.: 13093 Cov.: 31

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.412 AC: 62579 AN: 151782 Hom.: 13108 Cov.: 31 AF XY: 0.406 AC XY: 30084 AN XY: 74160

African (AFR) AF: 0.447 AC: 18499 AN: 41370

American (AMR) AF: 0.424 AC: 6455 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.392 AC: 1359 AN: 3468

East Asian (EAS) AF: 0.458 AC: 2357 AN: 5142

South Asian (SAS) AF: 0.347 AC: 1668 AN: 4806

European-Finnish (FIN) AF: 0.296 AC: 3114 AN: 10516

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.409 AC: 27798 AN: 67934

Other (OTH) AF: 0.399 AC: 840 AN: 2106

Alfa AF: 0.411 Hom.: 55776

Bravo AF: 0.425

Asia WGS AF: 0.395 AC: 1371 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.0
DANN	Benign	0.86
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs975405; hg19: chr4-123521180;