ENST00000769921.1:n.212-2469A>G

Variant names:

• chr15-45207849-A-G
• rs765787
• ENST00000769921.1:n.212-2469A>G

Variant summary

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

The ENST00000769921.1(ENSG00000300195):​n.212-2469A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 150,500 control chromosomes in the GnomAD database, including 2,180 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 0.15 (2180 hom., cov: 29)
• Consequence: ENSG00000300195 ENST00000769921.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 8 publications found

Genes affected

ENSG00000300195 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.294 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000769921.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000300195	ENST00000769921.1		n.212-2469A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.152 AC: 22922 AN: 150388 Hom.: 2180 Cov.: 29

Gnomad AFR AF: 0.0440

Gnomad AMI AF: 0.0861

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.159

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.152 AC: 22927 AN: 150500 Hom.: 2180 Cov.: 29 AF XY: 0.153 AC XY: 11236 AN XY: 73378

African (AFR) AF: 0.0439 AC: 1806 AN: 41128

American (AMR) AF: 0.216 AC: 3269 AN: 15122

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 647 AN: 3460

East Asian (EAS) AF: 0.307 AC: 1563 AN: 5092

South Asian (SAS) AF: 0.176 AC: 832 AN: 4724

European-Finnish (FIN) AF: 0.186 AC: 1865 AN: 10038

Middle Eastern (MID) AF: 0.154 AC: 45 AN: 292

European-Non Finnish (NFE) AF: 0.185 AC: 12481 AN: 67638

Other (OTH) AF: 0.162 AC: 341 AN: 2100

Alfa AF: 0.174 Hom.: 1411

Bravo AF: 0.149

Asia WGS AF: 0.218 AC: 760 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.7
DANN	Benign	0.72
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs765787; hg19: chr15-45500047;