rs8069976

Variant names:

• chr17-78353769-C-A
• rs8069976
• ENST00000794845.1:n.380G>T

Your query was ambiguous. Multiple possible variants found:

• chr17-78353769-C-A
• chr17-78353769-C-G

Variant summary

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

The ENST00000794845.1(ENSG00000303469):​n.380G>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 0.17 in 152,156 control chromosomes in the GnomAD database, including 2,291 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 0.17 (2291 hom., cov: 32)
• Consequence: ENSG00000303469 ENST00000794845.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00200
• Publications: 5 publications found

Genes affected

ENSG00000303469 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.171 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000794845.1. 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
	ENSG00000303469	ENST00000794845.1		n.380G>T		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000303484	ENST00000794921.1		n.732C>A		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000303469	ENST00000794841.1		n.138+1354G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25890 AN: 152036 Hom.: 2291 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.324

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.170 AC: 25892 AN: 152156 Hom.: 2291 Cov.: 32 AF XY: 0.170 AC XY: 12635 AN XY: 74388

African (AFR) AF: 0.171 AC: 7091 AN: 41504

American (AMR) AF: 0.142 AC: 2169 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.271 AC: 941 AN: 3470

East Asian (EAS) AF: 0.159 AC: 821 AN: 5164

South Asian (SAS) AF: 0.148 AC: 712 AN: 4824

European-Finnish (FIN) AF: 0.148 AC: 1565 AN: 10602

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.174 AC: 11835 AN: 67988

Other (OTH) AF: 0.184 AC: 389 AN: 2110

Alfa AF: 0.172 Hom.: 763

Bravo AF: 0.172

Asia WGS AF: 0.154 AC: 535 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	1.8
DANN	Benign	0.56
PhyloP100		-0.0020

Splicing

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

Other links and lift over

dbSNP: rs8069976; hg19: chr17-76349850;