ENST00000764486.1:n.590+4762A>G

Variant names:

• chr6-79783217-A-G
• rs721265
• ENST00000764486.1:n.590+4762A>G

Variant summary

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

The ENST00000764486.1(ENSG00000299545):​n.590+4762A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.399 in 152,160 control chromosomes in the GnomAD database, including 12,451 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 0.40 (12451 hom., cov: 33)
• Consequence: ENSG00000299545 ENST00000764486.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.979
• Publications: 2 publications found

Genes affected

ENSG00000299545 (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 (SAS) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000764486.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299545	ENST00000764486.1		n.590+4762A>G		intron	N/A
	ENSG00000299545	ENST00000764487.1		n.259+4762A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.399 AC: 60665 AN: 152040 Hom.: 12440 Cov.: 33

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.462

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.399 AC: 60704 AN: 152160 Hom.: 12451 Cov.: 33 AF XY: 0.398 AC XY: 29599 AN XY: 74378

African (AFR) AF: 0.360 AC: 14955 AN: 41520

American (AMR) AF: 0.375 AC: 5737 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.306 AC: 1061 AN: 3468

East Asian (EAS) AF: 0.202 AC: 1046 AN: 5186

South Asian (SAS) AF: 0.471 AC: 2267 AN: 4818

European-Finnish (FIN) AF: 0.462 AC: 4878 AN: 10562

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.433 AC: 29428 AN: 67996

Other (OTH) AF: 0.361 AC: 764 AN: 2114

Alfa AF: 0.426 Hom.: 8039

Bravo AF: 0.386

Asia WGS AF: 0.348 AC: 1213 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.50
DANN	Benign	0.43
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs721265; hg19: chr6-80492934;