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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000820561.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000306734	ENST00000820561.1		n.270+7542T>C		intron	N/A
	ENSG00000306734	ENST00000820562.1		n.266-4928T>C		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1780159;

hg19: chr9-15157977;