chr18-2104792-G-A

Variant names:

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

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371956	XR_935087.3	n.271+6852C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000263745	ENST00000579097.1	n.310+21408C>T		intron_variant	Intron 3 of 3	2
ENSG00000263745	ENST00000582086.2	n.93+6852C>T		intron_variant	Intron 1 of 3	2
ENSG00000263745	ENST00000584867.1	n.196+135001C>T		intron_variant	Intron 2 of 5	2

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 v4.3

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

Other links and lift over

dbSNP: rs566821; hg19: chr18-2104793;