chr17-78353915-T-G

Variant names:

• chr17-78353915-T-G
• rs8071356
• ENST00000794845.1:n.234A>C

Variant summary

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

The ENST00000794845.1(ENSG00000303469):​n.234A>C 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 0.171 in 152,100 control chromosomes in the GnomAD database, including 2,315 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 (2315 hom., cov: 32)
• Consequence: ENSG00000303469 ENST00000794845.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• 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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.172 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.234A>C		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000303469	ENST00000794841.1		n.138+1208A>C		intron	N/A
	ENSG00000303484	ENST00000794921.1		n.*113T>G		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.171 AC: 25995 AN: 151980 Hom.: 2314 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.324

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.171 AC: 25999 AN: 152100 Hom.: 2315 Cov.: 32 AF XY: 0.171 AC XY: 12684 AN XY: 74372

African (AFR) AF: 0.171 AC: 7112 AN: 41486

American (AMR) AF: 0.143 AC: 2191 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.271 AC: 940 AN: 3468

East Asian (EAS) AF: 0.161 AC: 832 AN: 5168

South Asian (SAS) AF: 0.149 AC: 719 AN: 4820

European-Finnish (FIN) AF: 0.148 AC: 1566 AN: 10590

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

European-Non Finnish (NFE) AF: 0.175 AC: 11880 AN: 67980

Other (OTH) AF: 0.185 AC: 391 AN: 2110

Alfa AF: 0.174 Hom.: 7783

Bravo AF: 0.173

Asia WGS AF: 0.158 AC: 548 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	0.097
DANN	Benign	0.40
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs8071356; hg19: chr17-76349996;