ENST00000820896.1:n.287C>G

Variant names:

• chr19-41641662-G-C
• rs1015758
• ENST00000820896.1:n.287C>G

Variant summary

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

The ENST00000820896.1(ENSG00000306768):​n.287C>G 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 0.211 in 152,142 control chromosomes in the GnomAD database, including 3,715 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 0.21 (3715 hom., cov: 32)
• Consequence: ENSG00000306768 ENST00000820896.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.163
• Publications: 2 publications found

Genes affected

ENSG00000306768 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000820896.1. 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
	ENSG00000306768	ENST00000820896.1		n.287C>G		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32103 AN: 152024 Hom.: 3715 Cov.: 32

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.00596

Gnomad SAS AF: 0.0988

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.236

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.211 AC: 32106 AN: 152142 Hom.: 3715 Cov.: 32 AF XY: 0.205 AC XY: 15231 AN XY: 74376

African (AFR) AF: 0.173 AC: 7184 AN: 41504

American (AMR) AF: 0.203 AC: 3110 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.257 AC: 893 AN: 3472

East Asian (EAS) AF: 0.00578 AC: 30 AN: 5188

South Asian (SAS) AF: 0.0997 AC: 481 AN: 4826

European-Finnish (FIN) AF: 0.179 AC: 1898 AN: 10580

Middle Eastern (MID) AF: 0.233 AC: 68 AN: 292

European-Non Finnish (NFE) AF: 0.260 AC: 17657 AN: 67968

Other (OTH) AF: 0.228 AC: 481 AN: 2114

Alfa AF: 0.128 Hom.: 240

Bravo AF: 0.215

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.4
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs1015758; hg19: chr19-42148030;