ENST00000685247.3:n.884-2786G>A

Variant names:

• chr6-32898134-G-A
• rs9276915
• ENST00000685247.3:n.884-2786G>A

Variant summary

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

The ENST00000685247.3(ENSG00000289047):​n.884-2786G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 152,110 control chromosomes in the GnomAD database, including 4,221 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 0.23 (4221 hom., cov: 31)
• Consequence: ENSG00000289047 ENST00000685247.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.139
• Publications: 20 publications found

Genes affected

ENSG00000289047 (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 (NFE) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000685247.3. 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
	LOC100294145	NR_037177.1		n.852-2786G>A		intron	N/A
	LOC100294145	NR_037178.1		n.753-2786G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289047	ENST00000685247.3		n.884-2786G>A		intron	N/A
	ENSG00000289047	ENST00000701517.2		n.684-2786G>A		intron	N/A
	ENSG00000289047	ENST00000753208.1		n.521-2786G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35274 AN: 151992 Hom.: 4225 Cov.: 31

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.232 AC: 35271 AN: 152110 Hom.: 4221 Cov.: 31 AF XY: 0.226 AC XY: 16835 AN XY: 74370

African (AFR) AF: 0.198 AC: 8230 AN: 41488

American (AMR) AF: 0.188 AC: 2876 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 747 AN: 3470

East Asian (EAS) AF: 0.198 AC: 1027 AN: 5180

South Asian (SAS) AF: 0.190 AC: 914 AN: 4816

European-Finnish (FIN) AF: 0.216 AC: 2285 AN: 10578

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.270 AC: 18353 AN: 67990

Other (OTH) AF: 0.250 AC: 527 AN: 2106

Alfa AF: 0.257 Hom.: 19037

Bravo AF: 0.227

Asia WGS AF: 0.201 AC: 703 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	6.0
DANN	Benign	0.43
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs9276915; hg19: chr6-32865911;