ENST00000847259.1:n.369-3093G>A

Variant names:

• chr17-56533930-C-T
• rs17760268
• ENST00000847259.1:n.369-3093G>A

Variant summary

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

The ENST00000847259.1(ENSG00000310109):​n.369-3093G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0564 in 152,316 control chromosomes in the GnomAD database, including 346 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 0.056 (346 hom., cov: 32)
• Consequence: ENSG00000310109 ENST00000847259.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.373
• Publications: 6 publications found

Genes affected

ENSG00000310109 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0842 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC112268194	XR_002958121.1	n.389-814G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000310109	ENST00000847259.1	n.369-3093G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0565 AC: 8592 AN: 152198 Hom.: 346 Cov.: 32

Gnomad AFR AF: 0.0159

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.0666

Gnomad ASJ AF: 0.0487

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0484

Gnomad FIN AF: 0.0365

Gnomad MID AF: 0.105

Gnomad NFE AF: 0.0861

Gnomad OTH AF: 0.0848

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

GnomAD4 genome AF: 0.0564 AC: 8586 AN: 152316 Hom.: 346 Cov.: 32 AF XY: 0.0545 AC XY: 4059 AN XY: 74488

African (AFR) AF: 0.0159 AC: 659 AN: 41564

American (AMR) AF: 0.0666 AC: 1019 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0487 AC: 169 AN: 3472

East Asian (EAS) AF: 0.000771 AC: 4 AN: 5186

South Asian (SAS) AF: 0.0480 AC: 232 AN: 4830

European-Finnish (FIN) AF: 0.0365 AC: 388 AN: 10624

Middle Eastern (MID) AF: 0.0993 AC: 29 AN: 292

European-Non Finnish (NFE) AF: 0.0861 AC: 5855 AN: 68030

Other (OTH) AF: 0.0839 AC: 177 AN: 2110

Alfa AF: 0.0674 Hom.: 320

Bravo AF: 0.0565

Asia WGS AF: 0.0210 AC: 72 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.72
DANN	Benign	0.60
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs17760268; hg19: chr17-54611291;