chr18-23027857-C-T

Variant names:

• chr18-23027857-C-T
• rs1010800

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 0.73 in 151,850 control chromosomes in the GnomAD database, including 40,827 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 0.73 (40827 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.651
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.773 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: 0.730 AC: 110819 AN: 151732 Hom.: 40802 Cov.: 30

Gnomad AFR AF: 0.673

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.691

Gnomad ASJ AF: 0.865

Gnomad EAS AF: 0.558

Gnomad SAS AF: 0.775

Gnomad FIN AF: 0.725

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.778

Gnomad OTH AF: 0.773

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

GnomAD4 genome AF: 0.730 AC: 110889 AN: 151850 Hom.: 40827 Cov.: 30 AF XY: 0.730 AC XY: 54162 AN XY: 74216

African (AFR) AF: 0.673 AC: 27859 AN: 41396

American (AMR) AF: 0.690 AC: 10510 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.865 AC: 2998 AN: 3466

East Asian (EAS) AF: 0.557 AC: 2871 AN: 5150

South Asian (SAS) AF: 0.775 AC: 3738 AN: 4822

European-Finnish (FIN) AF: 0.725 AC: 7629 AN: 10522

Middle Eastern (MID) AF: 0.898 AC: 264 AN: 294

European-Non Finnish (NFE) AF: 0.778 AC: 52872 AN: 67942

Other (OTH) AF: 0.770 AC: 1624 AN: 2108

Alfa AF: 0.770 Hom.: 75624

Bravo AF: 0.721

Asia WGS AF: 0.669 AC: 2326 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.20
DANN	Benign	0.18
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs1010800; hg19: chr18-20607820;