6-78316647-T-C

Variant names:

• chr6-78316647-T-C
• rs818284
• ENST00000715178.1:n.904-15826A>G

Variant summary

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

The ENST00000715178.1(ENSG00000230309):​n.904-15826A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.78 in 139,688 control chromosomes in the GnomAD database, including 46,792 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 0.78 (46792 hom., cov: 25)
• Consequence: ENSG00000230309 ENST00000715178.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.44
• Publications: 5 publications found

Genes affected

ENSG00000230309 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.921 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000715178.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000230309	ENST00000715178.1		n.904-15826A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.780 AC: 108908 AN: 139574 Hom.: 46787 Cov.: 25

Gnomad AFR AF: 0.562

Gnomad AMI AF: 0.941

Gnomad AMR AF: 0.735

Gnomad ASJ AF: 0.949

Gnomad EAS AF: 0.809

Gnomad SAS AF: 0.944

Gnomad FIN AF: 0.778

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.906

Gnomad OTH AF: 0.792

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

GnomAD4 genome AF: 0.780 AC: 108951 AN: 139688 Hom.: 46792 Cov.: 25 AF XY: 0.775 AC XY: 52660 AN XY: 67918

African (AFR) AF: 0.562 AC: 22335 AN: 39730

American (AMR) AF: 0.733 AC: 10408 AN: 14190

Ashkenazi Jewish (ASJ) AF: 0.949 AC: 3035 AN: 3198

East Asian (EAS) AF: 0.809 AC: 4091 AN: 5058

South Asian (SAS) AF: 0.945 AC: 4144 AN: 4386

European-Finnish (FIN) AF: 0.778 AC: 6678 AN: 8580

Middle Eastern (MID) AF: 0.902 AC: 231 AN: 256

European-Non Finnish (NFE) AF: 0.906 AC: 55769 AN: 61588

Other (OTH) AF: 0.792 AC: 1500 AN: 1894

Alfa AF: 0.831 Hom.: 6761

Asia WGS AF: 0.859 AC: 2932 AN: 3412

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.21
DANN	Benign	0.51
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs818284; hg19: chr6-79026364;