ENST00000755297.1:n.32+32833A>G

Variant names:

• chr6-31303939-A-G
• rs9461688
• ENST00000755297.1:n.32+32833A>G

Variant summary

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

The ENST00000755297.1(ENSG00000298396):​n.32+32833A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.338 in 151,874 control chromosomes in the GnomAD database, including 8,934 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 0.34 (8934 hom., cov: 32)
• Consequence: ENSG00000298396 ENST00000755297.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.330
• Publications: 24 publications found

Genes affected

ENSG00000298396 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC112267902	XR_926691.3	n.965-2085T>C		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298396	ENST00000755297.1	n.32+32833A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51249 AN: 151756 Hom.: 8925 Cov.: 32

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.338 AC: 51292 AN: 151874 Hom.: 8934 Cov.: 32 AF XY: 0.341 AC XY: 25305 AN XY: 74232

African (AFR) AF: 0.422 AC: 17461 AN: 41380

American (AMR) AF: 0.329 AC: 5026 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.309 AC: 1069 AN: 3464

East Asian (EAS) AF: 0.260 AC: 1343 AN: 5170

South Asian (SAS) AF: 0.370 AC: 1777 AN: 4808

European-Finnish (FIN) AF: 0.378 AC: 3985 AN: 10552

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.288 AC: 19566 AN: 67920

Other (OTH) AF: 0.336 AC: 709 AN: 2108

Alfa AF: 0.319 Hom.: 7779

Bravo AF: 0.337

Asia WGS AF: 0.298 AC: 1039 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	14
DANN	Benign	0.93
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs9461688; hg19: chr6-31271716;