ENST00000778316.1:n.385-30379G>A

Variant names:

• chr9-21306242-G-A
• rs12156640
• ENST00000778316.1:n.385-30379G>A

Variant summary

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

The ENST00000778316.1(ENSG00000301340):​n.385-30379G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0732 in 152,124 control chromosomes in the GnomAD database, including 498 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 0.073 (498 hom., cov: 32)
• Consequence: ENSG00000301340 ENST00000778316.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.62
• Publications: 9 publications found

Genes affected

ENSG00000301340 (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 (SAS) allele frequency at 95% confidence interval = 0.191 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107987053	XR_001746634.2	n.472-30379G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301340	ENST00000778316.1	n.385-30379G>A		intron_variant	Intron 2 of 2
ENSG00000301340	ENST00000778317.1	n.539-30379G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0732 AC: 11121 AN: 152006 Hom.: 498 Cov.: 32

Gnomad AFR AF: 0.0316

Gnomad AMI AF: 0.0934

Gnomad AMR AF: 0.0662

Gnomad ASJ AF: 0.0852

Gnomad EAS AF: 0.0439

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.0723

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0922

Gnomad OTH AF: 0.0712

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

GnomAD4 genome AF: 0.0732 AC: 11131 AN: 152124 Hom.: 498 Cov.: 32 AF XY: 0.0742 AC XY: 5521 AN XY: 74372

African (AFR) AF: 0.0316 AC: 1311 AN: 41520

American (AMR) AF: 0.0660 AC: 1008 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0852 AC: 295 AN: 3462

East Asian (EAS) AF: 0.0444 AC: 230 AN: 5180

South Asian (SAS) AF: 0.201 AC: 968 AN: 4808

European-Finnish (FIN) AF: 0.0723 AC: 765 AN: 10586

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0923 AC: 6272 AN: 67980

Other (OTH) AF: 0.0751 AC: 159 AN: 2116

Alfa AF: 0.0874 Hom.: 1375

Bravo AF: 0.0674

Asia WGS AF: 0.111 AC: 386 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	0.31
DANN	Benign	0.38
PhyloP100		-3.6

Splicing

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

Other links and lift over

dbSNP: rs12156640; hg19: chr9-21306241;