rs918837

Variant names:

• chr18-53886027-C-T
• rs918837

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 0.837 in 152,078 control chromosomes in the GnomAD database, including 54,042 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 0.84 (54042 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.781
• Publications: 2 publications found

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 (EAS) allele frequency at 95% confidence interval = 0.892 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: 0.837 AC: 127206 AN: 151960 Hom.: 54003 Cov.: 31

Gnomad AFR AF: 0.684

Gnomad AMI AF: 0.832

Gnomad AMR AF: 0.897

Gnomad ASJ AF: 0.822

Gnomad EAS AF: 0.913

Gnomad SAS AF: 0.911

Gnomad FIN AF: 0.896

Gnomad MID AF: 0.831

Gnomad NFE AF: 0.897

Gnomad OTH AF: 0.847

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

GnomAD4 genome AF: 0.837 AC: 127298 AN: 152078 Hom.: 54042 Cov.: 31 AF XY: 0.840 AC XY: 62429 AN XY: 74350

African (AFR) AF: 0.684 AC: 28329 AN: 41436

American (AMR) AF: 0.897 AC: 13702 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.822 AC: 2853 AN: 3472

East Asian (EAS) AF: 0.913 AC: 4724 AN: 5172

South Asian (SAS) AF: 0.912 AC: 4389 AN: 4814

European-Finnish (FIN) AF: 0.896 AC: 9488 AN: 10584

Middle Eastern (MID) AF: 0.832 AC: 243 AN: 292

European-Non Finnish (NFE) AF: 0.897 AC: 61027 AN: 68016

Other (OTH) AF: 0.848 AC: 1784 AN: 2104

Alfa AF: 0.876 Hom.: 74084

Bravo AF: 0.830

Asia WGS AF: 0.897 AC: 3119 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.58
DANN	Benign	0.36
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs918837; hg19: chr18-51412397;