ENST00000820533.1:n.327T>C

Variant names:

• chr17-8304837-A-G
• rs4792734
• ENST00000820533.1:n.327T>C

Variant summary

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

The ENST00000820533.1(ENSG00000226871):​n.327T>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 0.197 in 152,116 control chromosomes in the GnomAD database, including 4,413 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 0.20 (4413 hom., cov: 31)
• Consequence: ENSG00000226871 ENST00000820533.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.633
• Publications: 8 publications found

Genes affected

ENSG00000226871 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.606 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903915	XR_007065606.1	n.14T>C		non_coding_transcript_exon_variant	Exon 1 of 2
LOC124903914	XR_007065605.1	n.450-2A>G		splice_acceptor_variant, intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000226871	ENST00000820533.1	n.327T>C		non_coding_transcript_exon_variant	Exon 3 of 4
ENSG00000226871	ENST00000820534.1	n.226T>C		non_coding_transcript_exon_variant	Exon 2 of 3

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29914 AN: 151998 Hom.: 4399 Cov.: 31

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.624

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.0805

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.197 AC: 29957 AN: 152116 Hom.: 4413 Cov.: 31 AF XY: 0.203 AC XY: 15116 AN XY: 74366

African (AFR) AF: 0.326 AC: 13538 AN: 41486

American (AMR) AF: 0.279 AC: 4250 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 434 AN: 3472

East Asian (EAS) AF: 0.624 AC: 3226 AN: 5166

South Asian (SAS) AF: 0.169 AC: 814 AN: 4826

European-Finnish (FIN) AF: 0.157 AC: 1661 AN: 10606

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.0805 AC: 5475 AN: 68006

Other (OTH) AF: 0.185 AC: 390 AN: 2112

Alfa AF: 0.124 Hom.: 9871

Bravo AF: 0.216

Asia WGS AF: 0.360 AC: 1250 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.2
DANN	Benign	0.60
PhyloP100		0.63

Splicing

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

Other links and lift over

dbSNP: rs4792734; hg19: chr17-8208155;