ENST00000715587.1:n.1098+6931C>T

Variant names:

• chr18-75480491-C-T
• rs1865721
• ENST00000715587.1:n.1098+6931C>T

Variant summary

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

The ENST00000715587.1(ENSG00000287281):​n.1098+6931C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 151,894 control chromosomes in the GnomAD database, including 5,262 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 0.24 (5262 hom., cov: 31)
• Consequence: ENSG00000287281 ENST00000715587.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.99
• Publications: 8 publications found

Genes affected

ENSG00000287281 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.317 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000715587.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287281	ENST00000715587.1		n.1098+6931C>T		intron	N/A
	ENSG00000287281	ENST00000747311.1		n.376+6931C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36802 AN: 151776 Hom.: 5267 Cov.: 31

Gnomad AFR AF: 0.0843

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.242 AC: 36782 AN: 151894 Hom.: 5262 Cov.: 31 AF XY: 0.244 AC XY: 18090 AN XY: 74220

African (AFR) AF: 0.0840 AC: 3481 AN: 41448

American (AMR) AF: 0.219 AC: 3339 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.380 AC: 1318 AN: 3466

East Asian (EAS) AF: 0.194 AC: 1000 AN: 5142

South Asian (SAS) AF: 0.265 AC: 1269 AN: 4794

European-Finnish (FIN) AF: 0.351 AC: 3704 AN: 10542

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.320 AC: 21763 AN: 67916

Other (OTH) AF: 0.282 AC: 594 AN: 2108

Alfa AF: 0.280 Hom.: 10187

Bravo AF: 0.223

Asia WGS AF: 0.228 AC: 793 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.041
DANN	Benign	0.53
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs1865721; hg19: chr18-73192446;