chr9-79204129-G-A

Variant names:

• chr9-79204129-G-A
• rs2769965
• ENST00000722324.1:n.515+2722G>A

Variant summary

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

The ENST00000722324.1(ENSG00000294269):​n.515+2722G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.406 in 151,944 control chromosomes in the GnomAD database, including 13,257 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 0.41 (13257 hom., cov: 33)
• Consequence: ENSG00000294269 ENST00000722324.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.168
• Publications: 3 publications found

Genes affected

ENSG00000294269 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.586 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000722324.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000294269	ENST00000722324.1		n.515+2722G>A		intron	N/A
	ENSG00000294269	ENST00000722325.1		n.509-1989G>A		intron	N/A
	ENSG00000294269	ENST00000722326.1		n.424-2009G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.406 AC: 61589 AN: 151826 Hom.: 13250 Cov.: 33

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.328

Gnomad SAS AF: 0.603

Gnomad FIN AF: 0.462

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.406 AC: 61628 AN: 151944 Hom.: 13257 Cov.: 33 AF XY: 0.407 AC XY: 30239 AN XY: 74254

African (AFR) AF: 0.268 AC: 11113 AN: 41438

American (AMR) AF: 0.351 AC: 5360 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.383 AC: 1330 AN: 3470

East Asian (EAS) AF: 0.327 AC: 1687 AN: 5162

South Asian (SAS) AF: 0.604 AC: 2908 AN: 4814

European-Finnish (FIN) AF: 0.462 AC: 4864 AN: 10524

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.486 AC: 33041 AN: 67962

Other (OTH) AF: 0.385 AC: 811 AN: 2106

Alfa AF: 0.438 Hom.: 3514

Bravo AF: 0.388

Asia WGS AF: 0.482 AC: 1675 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.0
DANN	Benign	0.36
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs2769965; hg19: chr9-81819044;