6-32429626-T-G

Variant names:

• chr6-32429626-T-G
• rs9268585
• ENST00000766247.1:n.283-4466T>G

Variant summary

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

The ENST00000766247.1(ENSG00000299769):​n.283-4466T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.365 in 152,088 control chromosomes in the GnomAD database, including 10,593 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 0.37 (10593 hom., cov: 32)
• Consequence: ENSG00000299769 ENST00000766247.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.388
• Publications: 25 publications found

Genes affected

ENSG00000299769 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000766247.1. 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
	ENSG00000299769	ENST00000766247.1		n.283-4466T>G		intron	N/A
	ENSG00000299769	ENST00000766248.1		n.392-1088T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.366 AC: 55548 AN: 151970 Hom.: 10587 Cov.: 32

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.387

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

GnomAD4 genome AF: 0.365 AC: 55570 AN: 152088 Hom.: 10593 Cov.: 32 AF XY: 0.367 AC XY: 27315 AN XY: 74348

African (AFR) AF: 0.284 AC: 11765 AN: 41496

American (AMR) AF: 0.439 AC: 6704 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.517 AC: 1794 AN: 3470

East Asian (EAS) AF: 0.478 AC: 2464 AN: 5160

South Asian (SAS) AF: 0.511 AC: 2463 AN: 4818

European-Finnish (FIN) AF: 0.290 AC: 3061 AN: 10572

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.383 AC: 26003 AN: 67980

Other (OTH) AF: 0.390 AC: 824 AN: 2114

Alfa AF: 0.389 Hom.: 38354

Bravo AF: 0.371

Asia WGS AF: 0.445 AC: 1548 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.4
DANN	Benign	0.58
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs9268585; hg19: chr6-32397403;