ENST00000783298.1:n.388G>A

Variant names:

• chr18-43778617-C-T
• rs8085360
• ENST00000783298.1:n.388G>A

Variant summary

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

The ENST00000783298.1(ENSG00000302004):​n.388G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.441 in 151,832 control chromosomes in the GnomAD database, including 15,325 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 0.44 (15325 hom., cov: 31)
• Consequence: ENSG00000302004 ENST00000783298.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190
• Publications: 2 publications found

Genes affected

ENSG00000302004 (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 (NFE) allele frequency at 95% confidence interval = 0.496 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000783298.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000302004	ENST00000783298.1		n.388G>A		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.442 AC: 66984 AN: 151714 Hom.: 15319 Cov.: 31

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.517

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.441 AC: 67005 AN: 151832 Hom.: 15325 Cov.: 31 AF XY: 0.439 AC XY: 32537 AN XY: 74160

African (AFR) AF: 0.388 AC: 16085 AN: 41408

American (AMR) AF: 0.368 AC: 5614 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.544 AC: 1881 AN: 3460

East Asian (EAS) AF: 0.111 AC: 575 AN: 5166

South Asian (SAS) AF: 0.424 AC: 2038 AN: 4810

European-Finnish (FIN) AF: 0.517 AC: 5427 AN: 10504

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.500 AC: 33980 AN: 67920

Other (OTH) AF: 0.432 AC: 908 AN: 2100

Alfa AF: 0.484 Hom.: 3970

Bravo AF: 0.425

Asia WGS AF: 0.277 AC: 972 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	4.9
DANN	Benign	0.66
PhyloP100		0.019

Splicing

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

Other links and lift over

dbSNP: rs8085360; hg19: chr18-41358582;