ENST00000591869.1:n.228+15417G>C

Variant names:

• chr18-60715469-C-G
• rs931078
• ENST00000591869.1:n.228+15417G>C

Variant summary

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

The ENST00000591869.1(ENSG00000267098):​n.228+15417G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.445 in 151,834 control chromosomes in the GnomAD database, including 16,243 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 0.45 (16243 hom., cov: 31)
• Consequence: ENSG00000267098 ENST00000591869.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.127
• Publications: 2 publications found

Genes affected

ENSG00000267098 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.612 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
ENSG00000267098	ENST00000591869.1	n.228+15417G>C		intron_variant	Intron 5 of 7	4
ENSG00000267098	ENST00000655645.1	n.164+15417G>C		intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes AF: 0.446 AC: 67600 AN: 151716 Hom.: 16236 Cov.: 31

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.640

Gnomad EAS AF: 0.630

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.509

Gnomad OTH AF: 0.485

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

GnomAD4 genome AF: 0.445 AC: 67631 AN: 151834 Hom.: 16243 Cov.: 31 AF XY: 0.448 AC XY: 33251 AN XY: 74214

African (AFR) AF: 0.263 AC: 10901 AN: 41402

American (AMR) AF: 0.464 AC: 7068 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.640 AC: 2218 AN: 3468

East Asian (EAS) AF: 0.630 AC: 3248 AN: 5152

South Asian (SAS) AF: 0.596 AC: 2858 AN: 4796

European-Finnish (FIN) AF: 0.488 AC: 5149 AN: 10554

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.509 AC: 34547 AN: 67926

Other (OTH) AF: 0.488 AC: 1027 AN: 2104

Alfa AF: 0.471 Hom.: 2206

Bravo AF: 0.435

Asia WGS AF: 0.599 AC: 2084 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.7
DANN	Benign	0.64
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs931078; hg19: chr18-58382702;