9-79042279-A-G

Variant names:

• chr9-79042279-A-G
• rs10512080
• ENST00000756624.1:n.82-2777A>G

Variant summary

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

The ENST00000756624.1(ENSG00000298572):​n.82-2777A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.646 in 152,036 control chromosomes in the GnomAD database, including 33,481 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 0.65 (33481 hom., cov: 33)
• Consequence: ENSG00000298572 ENST00000756624.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.317
• Publications: 3 publications found

Genes affected

ENSG00000298572 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.748 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
ENSG00000298572	ENST00000756624.1	n.82-2777A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.647 AC: 98250 AN: 151918 Hom.: 33476 Cov.: 33

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.849

Gnomad AMR AF: 0.638

Gnomad ASJ AF: 0.801

Gnomad EAS AF: 0.714

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.766

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.754

Gnomad OTH AF: 0.667

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

GnomAD4 genome AF: 0.646 AC: 98273 AN: 152036 Hom.: 33481 Cov.: 33 AF XY: 0.649 AC XY: 48214 AN XY: 74316

African (AFR) AF: 0.414 AC: 17150 AN: 41466

American (AMR) AF: 0.638 AC: 9732 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.801 AC: 2782 AN: 3472

East Asian (EAS) AF: 0.714 AC: 3702 AN: 5188

South Asian (SAS) AF: 0.668 AC: 3219 AN: 4816

European-Finnish (FIN) AF: 0.766 AC: 8087 AN: 10564

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.754 AC: 51228 AN: 67958

Other (OTH) AF: 0.669 AC: 1408 AN: 2106

Alfa AF: 0.709 Hom.: 74991

Bravo AF: 0.627

Asia WGS AF: 0.672 AC: 2326 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.39
DANN	Benign	0.58
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs10512080; hg19: chr9-81657195;