8-116604462-C-T

Variant names:

• chr8-116604462-C-T
• rs1317644
• ENST00000806232.1:n.5C>T

Variant summary

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

The ENST00000806232.1(ENSG00000304777):​n.5C>T 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 0.812 in 152,098 control chromosomes in the GnomAD database, including 50,316 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 0.81 (50316 hom., cov: 31)
• Consequence: ENSG00000304777 ENST00000806232.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• Publications: 4 publications found

Genes affected

ENSG00000304777 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.843 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000806232.1. 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
	ENSG00000304777	ENST00000806232.1		n.5C>T		non_coding_transcript_exon	Exon 1 of 3
	ENSG00000304777	ENST00000806227.1		n.138+79C>T		intron	N/A
	ENSG00000304777	ENST00000806231.1		n.177+79C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.812 AC: 123475 AN: 151980 Hom.: 50302 Cov.: 31

Gnomad AFR AF: 0.752

Gnomad AMI AF: 0.808

Gnomad AMR AF: 0.800

Gnomad ASJ AF: 0.789

Gnomad EAS AF: 0.809

Gnomad SAS AF: 0.794

Gnomad FIN AF: 0.850

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.849

Gnomad OTH AF: 0.805

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

GnomAD4 genome AF: 0.812 AC: 123536 AN: 152098 Hom.: 50316 Cov.: 31 AF XY: 0.812 AC XY: 60345 AN XY: 74360

African (AFR) AF: 0.752 AC: 31172 AN: 41458

American (AMR) AF: 0.800 AC: 12223 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.789 AC: 2737 AN: 3470

East Asian (EAS) AF: 0.808 AC: 4160 AN: 5148

South Asian (SAS) AF: 0.794 AC: 3832 AN: 4826

European-Finnish (FIN) AF: 0.850 AC: 9013 AN: 10600

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.849 AC: 57736 AN: 68004

Other (OTH) AF: 0.805 AC: 1700 AN: 2112

Alfa AF: 0.835 Hom.: 232301

Bravo AF: 0.804

Asia WGS AF: 0.787 AC: 2738 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.078
DANN	Benign	0.56
PhyloP100		-1.2

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1317644;

hg19: chr8-117616701;