ENST00000567777.1:n.139-67390G>A

Variant names:

• chr16-76844965-G-A
• rs13330107
• ENST00000567777.1:n.139-67390G>A

Variant summary

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

The ENST00000567777.1(ENSG00000259995):​n.139-67390G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.352 in 151,982 control chromosomes in the GnomAD database, including 9,523 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 0.35 (9523 hom., cov: 32)
• Consequence: ENSG00000259995 ENST00000567777.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.231

Genes affected

ENSG00000259995 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.371 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
ENSG00000259995	ENST00000567777.1	n.139-67390G>A		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.352 AC: 53528 AN: 151864 Hom.: 9514 Cov.: 32

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.415

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.352 AC: 53567 AN: 151982 Hom.: 9523 Cov.: 32 AF XY: 0.345 AC XY: 25598 AN XY: 74290

Gnomad4 AFR AF: 0.376

Gnomad4 AMR AF: 0.279

Gnomad4 ASJ AF: 0.415

Gnomad4 EAS AF: 0.334

Gnomad4 SAS AF: 0.253

Gnomad4 FIN AF: 0.284

Gnomad4 NFE AF: 0.370

Gnomad4 OTH AF: 0.370

Alfa AF: 0.366 Hom.: 18592

Bravo AF: 0.354

Asia WGS AF: 0.350 AC: 1219 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.50
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13330107; hg19: chr16-76878862;