rs1800813

Variant names:

• chr4-54228300-G-A
• rs1800813
• ENST00000507166.5:c.1018-46625G>A

Variant summary

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

The ENST00000507166.5(ENSG00000282278):​c.1018-46625G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 152,084 control chromosomes in the GnomAD database, including 3,500 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 0.21 (3500 hom., cov: 32)
• Consequence: ENSG00000282278 ENST00000507166.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.432
• Publications: 17 publications found

Genes affected

ENSG00000282278 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.309 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000282278	ENST00000507166.5	c.1018-46625G>A		intron_variant	Intron 12 of 23	2		ENSP00000423325.1

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31673 AN: 151966 Hom.: 3500 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.0957

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.208 AC: 31687 AN: 152084 Hom.: 3500 Cov.: 32 AF XY: 0.211 AC XY: 15658 AN XY: 74344

African (AFR) AF: 0.178 AC: 7389 AN: 41492

American (AMR) AF: 0.316 AC: 4836 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0957 AC: 332 AN: 3470

East Asian (EAS) AF: 0.198 AC: 1021 AN: 5148

South Asian (SAS) AF: 0.250 AC: 1201 AN: 4812

European-Finnish (FIN) AF: 0.206 AC: 2179 AN: 10576

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.208 AC: 14171 AN: 67986

Other (OTH) AF: 0.182 AC: 385 AN: 2110

Alfa AF: 0.205 Hom.: 5546

Bravo AF: 0.215

Asia WGS AF: 0.241 AC: 839 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	10
DANN	Benign	0.86
PhyloP100		0.43
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1800813; hg19: chr4-55094467;