chr9-79808879-G-A

Variant names:

• chr9-79808879-G-A
• rs1114559
• ENST00000809831.1:n.104-3609G>A

Variant summary

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

The ENST00000809831.1(ENSG00000305253):​n.104-3609G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.811 in 152,088 control chromosomes in the GnomAD database, including 50,466 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 0.81 (50466 hom., cov: 31)
• Consequence: ENSG00000305253 ENST00000809831.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.68
• Publications: 2 publications found

Genes affected

ENSG00000305253 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.891 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
ENSG00000305253	ENST00000809831.1	n.104-3609G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.811 AC: 123273 AN: 151970 Hom.: 50422 Cov.: 31

Gnomad AFR AF: 0.899

Gnomad AMI AF: 0.657

Gnomad AMR AF: 0.751

Gnomad ASJ AF: 0.818

Gnomad EAS AF: 0.696

Gnomad SAS AF: 0.728

Gnomad FIN AF: 0.772

Gnomad MID AF: 0.879

Gnomad NFE AF: 0.794

Gnomad OTH AF: 0.805

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

GnomAD4 genome AF: 0.811 AC: 123368 AN: 152088 Hom.: 50466 Cov.: 31 AF XY: 0.808 AC XY: 60030 AN XY: 74332

African (AFR) AF: 0.898 AC: 37305 AN: 41524

American (AMR) AF: 0.751 AC: 11472 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.818 AC: 2837 AN: 3468

East Asian (EAS) AF: 0.695 AC: 3589 AN: 5164

South Asian (SAS) AF: 0.727 AC: 3502 AN: 4816

European-Finnish (FIN) AF: 0.772 AC: 8154 AN: 10558

Middle Eastern (MID) AF: 0.884 AC: 258 AN: 292

European-Non Finnish (NFE) AF: 0.794 AC: 53949 AN: 67968

Other (OTH) AF: 0.808 AC: 1704 AN: 2110

Alfa AF: 0.798 Hom.: 18956

Bravo AF: 0.812

Asia WGS AF: 0.720 AC: 2504 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.012
DANN	Benign	0.65
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs1114559; hg19: chr9-82423794; COSMIC: COSV60364169;