rs9784758

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 21 publications found

Genes affected

ENSG00000250264 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000307274	ENST00000824890.1	n.-68T>C		upstream_gene_variant
ENSG00000307274	ENST00000824891.1	n.-67T>C		upstream_gene_variant
ENSG00000307274	ENST00000824892.1	n.-71T>C		upstream_gene_variant

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

African (AFR) AF: 0.223 AC: 9254 AN: 41464

American (AMR) AF: 0.0713 AC: 1090 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0620 AC: 215 AN: 3470

East Asian (EAS) AF: 0.0620 AC: 321 AN: 5180

South Asian (SAS) AF: 0.0944 AC: 456 AN: 4828

European-Finnish (FIN) AF: 0.101 AC: 1074 AN: 10610

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.0593 AC: 4032 AN: 68010

Other (OTH) AF: 0.0995 AC: 210 AN: 2110

Alfa AF: 0.0851 Hom.: 1965

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
PhyloP100		-0.094
PromoterAI		-0.036	Neutral

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

Other links and lift over

dbSNP: rs9784758; hg19: chr6-32788511;