ENST00000748761.1:n.293+15679C>T

Variant names:

• chr18-66242447-G-A
• rs1565516
• ENST00000748761.1:n.293+15679C>T

Variant summary

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

The ENST00000748761.1(ENSG00000297542):​n.293+15679C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0915 in 149,780 control chromosomes in the GnomAD database, including 1,573 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 0.091 (1573 hom., cov: 31)
• Consequence: ENSG00000297542 ENST00000748761.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.953
• Publications: 2 publications found

Genes affected

ENSG00000297542 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.216 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
ENSG00000297542	ENST00000748761.1	n.293+15679C>T		intron_variant	Intron 1 of 1
ENSG00000297542	ENST00000748762.1	n.278-1361C>T		intron_variant	Intron 1 of 2
ENSG00000297563	ENST00000748921.1	n.155+122G>A		intron_variant	Intron 1 of 1
ENSG00000297563	ENST00000748922.1	n.133+122G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0914 AC: 13682 AN: 149668 Hom.: 1573 Cov.: 31

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.0509

Gnomad AMR AF: 0.0559

Gnomad ASJ AF: 0.0539

Gnomad EAS AF: 0.0120

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.00863

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0383

Gnomad OTH AF: 0.0976

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

GnomAD4 genome AF: 0.0915 AC: 13698 AN: 149780 Hom.: 1573 Cov.: 31 AF XY: 0.0902 AC XY: 6600 AN XY: 73140

African (AFR) AF: 0.220 AC: 9066 AN: 41300

American (AMR) AF: 0.0558 AC: 818 AN: 14668

Ashkenazi Jewish (ASJ) AF: 0.0539 AC: 184 AN: 3416

East Asian (EAS) AF: 0.0120 AC: 62 AN: 5170

South Asian (SAS) AF: 0.137 AC: 633 AN: 4636

European-Finnish (FIN) AF: 0.00863 AC: 89 AN: 10316

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0383 AC: 2564 AN: 67004

Other (OTH) AF: 0.101 AC: 210 AN: 2072

Alfa AF: 0.0279 Hom.: 76

Asia WGS AF: 0.0960 AC: 334 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.79
PhyloP100		0.95

Splicing

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

Other links and lift over

dbSNP: rs1565516; hg19: chr18-63909684;