rs4800613

Variant names:

• chr18-25027759-G-A
• rs4800613

Your query was ambiguous. Multiple possible variants found:

• chr18-25027759-G-A
• chr18-25027759-G-C

Variant summary

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

The variant allele was found at a frequency of 0.625 in 152,038 control chromosomes in the GnomAD database, including 30,385 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 0.63 (30385 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.470
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.694 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

Frequencies

GnomAD3 genomes AF: 0.626 AC: 95046 AN: 151920 Hom.: 30392 Cov.: 33

Gnomad AFR AF: 0.498

Gnomad AMI AF: 0.705

Gnomad AMR AF: 0.668

Gnomad ASJ AF: 0.695

Gnomad EAS AF: 0.606

Gnomad SAS AF: 0.626

Gnomad FIN AF: 0.563

Gnomad MID AF: 0.736

Gnomad NFE AF: 0.699

Gnomad OTH AF: 0.658

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

GnomAD4 genome AF: 0.625 AC: 95072 AN: 152038 Hom.: 30385 Cov.: 33 AF XY: 0.620 AC XY: 46104 AN XY: 74312

African (AFR) AF: 0.498 AC: 20632 AN: 41462

American (AMR) AF: 0.668 AC: 10209 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.695 AC: 2411 AN: 3470

East Asian (EAS) AF: 0.606 AC: 3121 AN: 5152

South Asian (SAS) AF: 0.624 AC: 3012 AN: 4824

European-Finnish (FIN) AF: 0.563 AC: 5940 AN: 10552

Middle Eastern (MID) AF: 0.726 AC: 212 AN: 292

European-Non Finnish (NFE) AF: 0.699 AC: 47501 AN: 67972

Other (OTH) AF: 0.658 AC: 1392 AN: 2114

Alfa AF: 0.677 Hom.: 156665

Bravo AF: 0.627

Asia WGS AF: 0.611 AC: 2126 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	6.7
DANN	Benign	0.56
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs4800613; hg19: chr18-22607723;