rs566821

Variant names:

• chr18-2104792-G-A
• rs566821
• ENST00000579097.1:n.310+21408C>T

Your query was ambiguous. Multiple possible variants found:

• chr18-2104792-G-A
• chr18-2104792-G-C

Variant summary

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

The ENST00000579097.1(ENSG00000263745):​n.310+21408C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.865 in 151,016 control chromosomes in the GnomAD database, including 56,836 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 0.87 (56836 hom., cov: 26)
• Consequence: ENSG00000263745 ENST00000579097.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0630
• Publications: 2 publications found

Genes affected

ENSG00000263745 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.963 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000579097.1. 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
	ENSG00000263745	ENST00000579097.1	TSL:2	n.310+21408C>T		intron	N/A
	ENSG00000263745	ENST00000582086.2	TSL:2	n.93+6852C>T		intron	N/A
	ENSG00000263745	ENST00000584867.1	TSL:2	n.196+135001C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.865 AC: 130569 AN: 150898 Hom.: 56780 Cov.: 26

Gnomad AFR AF: 0.950

Gnomad AMI AF: 0.765

Gnomad AMR AF: 0.883

Gnomad ASJ AF: 0.848

Gnomad EAS AF: 0.986

Gnomad SAS AF: 0.861

Gnomad FIN AF: 0.887

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.801

Gnomad OTH AF: 0.855

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

GnomAD4 genome AF: 0.865 AC: 130685 AN: 151016 Hom.: 56836 Cov.: 26 AF XY: 0.870 AC XY: 64115 AN XY: 73684

African (AFR) AF: 0.950 AC: 38984 AN: 41054

American (AMR) AF: 0.884 AC: 13394 AN: 15158

Ashkenazi Jewish (ASJ) AF: 0.848 AC: 2931 AN: 3458

East Asian (EAS) AF: 0.986 AC: 5027 AN: 5100

South Asian (SAS) AF: 0.861 AC: 4107 AN: 4772

European-Finnish (FIN) AF: 0.887 AC: 9131 AN: 10296

Middle Eastern (MID) AF: 0.857 AC: 252 AN: 294

European-Non Finnish (NFE) AF: 0.801 AC: 54358 AN: 67868

Other (OTH) AF: 0.857 AC: 1805 AN: 2106

Alfa AF: 0.832 Hom.: 94716

Bravo AF: 0.870

Asia WGS AF: 0.941 AC: 3274 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.7
DANN	Benign	0.50
PhyloP100		-0.063

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: rs566821;

hg19: chr18-2104793;