rs2239857

Variant names:

• chr16-82626338-C-G
• rs2239857
• ENST00000793365.1:n.972G>C

Your query was ambiguous. Multiple possible variants found:

• chr16-82626338-C-G
• chr16-82626338-C-T

Variant summary

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

The ENST00000793365.1(ENSG00000303284):​n.972G>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 0.048 in 152,204 control chromosomes in the GnomAD database, including 454 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 0.048 (454 hom., cov: 33)
• Consequence: ENSG00000303284 ENST00000793365.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.116
• Publications: 4 publications found

Genes affected

ENSG00000303284 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.32 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000793365.1. 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
	ENSG00000303284	ENST00000793365.1		n.972G>C		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0480 AC: 7302 AN: 152086 Hom.: 455 Cov.: 33

Gnomad AFR AF: 0.0590

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0322

Gnomad ASJ AF: 0.00691

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.0906

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0147

Gnomad OTH AF: 0.0378

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

GnomAD4 genome AF: 0.0480 AC: 7303 AN: 152204 Hom.: 454 Cov.: 33 AF XY: 0.0548 AC XY: 4079 AN XY: 74408

African (AFR) AF: 0.0592 AC: 2458 AN: 41542

American (AMR) AF: 0.0322 AC: 492 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.00691 AC: 24 AN: 3472

East Asian (EAS) AF: 0.333 AC: 1717 AN: 5154

South Asian (SAS) AF: 0.0895 AC: 431 AN: 4818

European-Finnish (FIN) AF: 0.104 AC: 1102 AN: 10590

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0147 AC: 997 AN: 68014

Other (OTH) AF: 0.0379 AC: 80 AN: 2112

Alfa AF: 0.0155 Hom.: 7

Bravo AF: 0.0445

Asia WGS AF: 0.188 AC: 652 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.29
DANN	Benign	0.26
PhyloP100		0.12

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: rs2239857;

hg19: chr16-82659943;