rs4800820

Variant names:

• chr18-27796509-C-T
• rs4800820
• ENST00000750368.1:n.495+1027G>A

Variant summary

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

The ENST00000750368.1(ENSG00000297707):​n.495+1027G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.54 in 151,970 control chromosomes in the GnomAD database, including 24,566 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 0.54 (24566 hom., cov: 33)
• Consequence: ENSG00000297707 ENST00000750368.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.241
• Publications: 3 publications found

Genes affected

ENSG00000297707 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.65 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000750368.1. 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
	ENSG00000297707	ENST00000750368.1		n.495+1027G>A		intron	N/A
	ENSG00000286426	ENST00000750547.1		n.481-6412C>T		intron	N/A
	ENSG00000286426	ENST00000750548.1		n.472+5247C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.540 AC: 82072 AN: 151852 Hom.: 24560 Cov.: 33

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.656

Gnomad AMR AF: 0.648

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.566

Gnomad FIN AF: 0.699

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.655

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.540 AC: 82095 AN: 151970 Hom.: 24566 Cov.: 33 AF XY: 0.545 AC XY: 40464 AN XY: 74268

African (AFR) AF: 0.269 AC: 11160 AN: 41414

American (AMR) AF: 0.649 AC: 9914 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.595 AC: 2064 AN: 3468

East Asian (EAS) AF: 0.466 AC: 2407 AN: 5162

South Asian (SAS) AF: 0.566 AC: 2728 AN: 4824

European-Finnish (FIN) AF: 0.699 AC: 7369 AN: 10546

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.655 AC: 44507 AN: 67954

Other (OTH) AF: 0.552 AC: 1166 AN: 2114

Alfa AF: 0.620 Hom.: 126509

Bravo AF: 0.522

Asia WGS AF: 0.510 AC: 1772 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.2
DANN	Benign	0.58
PhyloP100		0.24

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: rs4800820;

hg19: chr18-25376473;

COSMIC: COSV69621225;