ENST00000780853.1:n.188-9493G>A

Variant names:

• chr15-32217691-C-T
• rs2926504
• ENST00000780853.1:n.188-9493G>A

Variant summary

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

The ENST00000780853.1(ENSG00000301688):​n.188-9493G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.714 in 151,376 control chromosomes in the GnomAD database, including 39,402 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 0.71 (39402 hom., cov: 33)
• Consequence: ENSG00000301688 ENST00000780853.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.725
• Publications: 7 publications found

Genes affected

ENSG00000301688 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.898 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102724078	XR_007064559.1	n.448-9493G>A		intron_variant	Intron 2 of 9
LOC102724078	XR_007064560.1	n.448-9493G>A		intron_variant	Intron 2 of 9
LOC102724078	XR_007064561.1	n.527-9493G>A		intron_variant	Intron 2 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301688	ENST00000780853.1	n.188-9493G>A		intron_variant	Intron 2 of 8
ENSG00000301688	ENST00000780854.1	n.241-9493G>A		intron_variant	Intron 2 of 5
ENSG00000301688	ENST00000780855.1	n.188-9493G>A		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.714 AC: 107955 AN: 151264 Hom.: 39381 Cov.: 33

Gnomad AFR AF: 0.591

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.714

Gnomad ASJ AF: 0.793

Gnomad EAS AF: 0.874

Gnomad SAS AF: 0.921

Gnomad FIN AF: 0.796

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.744

Gnomad OTH AF: 0.729

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

GnomAD4 genome AF: 0.714 AC: 108028 AN: 151376 Hom.: 39402 Cov.: 33 AF XY: 0.721 AC XY: 53344 AN XY: 73942

African (AFR) AF: 0.591 AC: 24290 AN: 41110

American (AMR) AF: 0.714 AC: 10847 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.793 AC: 2751 AN: 3470

East Asian (EAS) AF: 0.875 AC: 4486 AN: 5128

South Asian (SAS) AF: 0.921 AC: 4422 AN: 4802

European-Finnish (FIN) AF: 0.796 AC: 8327 AN: 10464

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.744 AC: 50523 AN: 67900

Other (OTH) AF: 0.733 AC: 1540 AN: 2102

Alfa AF: 0.727 Hom.: 70611

Bravo AF: 0.701

Asia WGS AF: 0.881 AC: 3037 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.82
DANN	Benign	0.72
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs2926504; hg19: chr15-32509892;