ENST00000782918.1:n.155+9065C>A

Variant names:

• chr6-86928621-G-T
• rs9450594
• ENST00000782918.1:n.155+9065C>A

Variant summary

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

The ENST00000782918.1(ENSG00000301924):​n.155+9065C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 152,064 control chromosomes in the GnomAD database, including 2,406 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 0.15 (2406 hom., cov: 32)
• Consequence: ENSG00000301924 ENST00000782918.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.619
• Publications: 2 publications found

Genes affected

ENSG00000301924 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.29 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
ENSG00000301924	ENST00000782918.1	n.155+9065C>A		intron_variant	Intron 1 of 2
ENSG00000301924	ENST00000782919.1	n.383+160C>A		intron_variant	Intron 3 of 4
ENSG00000301924	ENST00000782920.1	n.165+8812C>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23339 AN: 151948 Hom.: 2390 Cov.: 32

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.0975

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.0469

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.0673

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.154 AC: 23405 AN: 152064 Hom.: 2406 Cov.: 32 AF XY: 0.151 AC XY: 11241 AN XY: 74334

African (AFR) AF: 0.294 AC: 12190 AN: 41442

American (AMR) AF: 0.0973 AC: 1486 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.106 AC: 367 AN: 3470

East Asian (EAS) AF: 0.0470 AC: 244 AN: 5188

South Asian (SAS) AF: 0.142 AC: 685 AN: 4816

European-Finnish (FIN) AF: 0.0673 AC: 712 AN: 10580

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.106 AC: 7235 AN: 67980

Other (OTH) AF: 0.146 AC: 308 AN: 2114

Alfa AF: 0.114 Hom.: 2620

Bravo AF: 0.160

Asia WGS AF: 0.114 AC: 396 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.20
DANN	Benign	0.13
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs9450594; hg19: chr6-87638339;