rs9784758

Variant names:

• chr6-32820734-T-C
• rs9784758
• ENST00000452392.2:c.1933-3782A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000452392.2(ENSG00000250264):​c.1933-3782A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,172 control chromosomes in the GnomAD database, including 1,290 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 0.11 (1290 hom., cov: 32)
• Consequence: ENSG00000250264 ENST00000452392.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0940

Genes affected

ENSG00000250264 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.219 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000250264	ENST00000452392.2	c.1933-3782A>G		intron_variant	Intron 11 of 14	2		ENSP00000391806.2

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16718 AN: 152054 Hom.: 1287 Cov.: 32

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.0714

Gnomad ASJ AF: 0.0620

Gnomad EAS AF: 0.0618

Gnomad SAS AF: 0.0938

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0593

Gnomad OTH AF: 0.0977

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

GnomAD4 genome AF: 0.110 AC: 16745 AN: 152172 Hom.: 1290 Cov.: 32 AF XY: 0.111 AC XY: 8267 AN XY: 74420

Gnomad4 AFR AF: 0.223

Gnomad4 AMR AF: 0.0713

Gnomad4 ASJ AF: 0.0620

Gnomad4 EAS AF: 0.0620

Gnomad4 SAS AF: 0.0944

Gnomad4 FIN AF: 0.101

Gnomad4 NFE AF: 0.0593

Gnomad4 OTH AF: 0.0995

Alfa AF: 0.0773 Hom.: 426

Bravo AF: 0.112

Asia WGS AF: 0.0810 AC: 282 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.47

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs9784758; hg19: chr6-32788511;