rs1780159

Variant names:

• chr9-15157979-T-C
• rs1780159
• ENST00000820561.1:n.270+7542T>C

Variant summary

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

The ENST00000820561.1(ENSG00000306734):​n.270+7542T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0779 in 151,056 control chromosomes in the GnomAD database, including 706 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 0.078 (706 hom., cov: 32)
• Consequence: ENSG00000306734 ENST00000820561.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.267
• Publications: 8 publications found

Genes affected

ENSG00000306734 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0843 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902123	XR_007061423.1	n.236-4928T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000306734	ENST00000820561.1	n.270+7542T>C		intron_variant	Intron 2 of 2
ENSG00000306734	ENST00000820562.1	n.266-4928T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.0779 AC: 11751 AN: 150938 Hom.: 704 Cov.: 32

Gnomad AFR AF: 0.0818

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.0483

Gnomad ASJ AF: 0.0346

Gnomad EAS AF: 0.0779

Gnomad SAS AF: 0.0505

Gnomad FIN AF: 0.0724

Gnomad MID AF: 0.0637

Gnomad NFE AF: 0.0861

Gnomad OTH AF: 0.0618

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

GnomAD4 genome AF: 0.0779 AC: 11762 AN: 151056 Hom.: 706 Cov.: 32 AF XY: 0.0759 AC XY: 5607 AN XY: 73852

African (AFR) AF: 0.0818 AC: 3304 AN: 40410

American (AMR) AF: 0.0482 AC: 736 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.0346 AC: 120 AN: 3472

East Asian (EAS) AF: 0.0781 AC: 405 AN: 5184

South Asian (SAS) AF: 0.0505 AC: 244 AN: 4828

European-Finnish (FIN) AF: 0.0724 AC: 768 AN: 10608

Middle Eastern (MID) AF: 0.0719 AC: 21 AN: 292

European-Non Finnish (NFE) AF: 0.0861 AC: 5856 AN: 68002

Other (OTH) AF: 0.0611 AC: 128 AN: 2094

Alfa AF: 0.0798 Hom.: 1888

Bravo AF: 0.0766

Asia WGS AF: 0.0540 AC: 186 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	5.4
DANN	Benign	0.94
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs1780159; hg19: chr9-15157977;