rs2769965

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902186	XR_007061599.1	n.201+2722G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000294269	ENST00000722324.1	n.515+2722G>A		intron_variant	Intron 2 of 2
ENSG00000294269	ENST00000722325.1	n.509-1989G>A		intron_variant	Intron 2 of 2
ENSG00000294269	ENST00000722326.1	n.424-2009G>A		intron_variant	Intron 2 of 2

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 v4.3

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;