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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372042	XR_935323.3	n.695+5247C>T		intron_variant	Intron 3 of 4
LOC105372042	XR_935324.3	n.628-6412C>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297707	ENST00000750368.1	n.495+1027G>A		intron_variant	Intron 2 of 4
ENSG00000286426	ENST00000750547.1	n.481-6412C>T		intron_variant	Intron 2 of 3
ENSG00000286426	ENST00000750548.1	n.472+5247C>T		intron_variant	Intron 3 of 4

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 v4.3

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

Other links and lift over

dbSNP: rs4800820; hg19: chr18-25376473; COSMIC: COSV69621225;