rs4918818

Variant names:

• chr10-113409163-C-A
• rs4918818

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 0.122 in 152,266 control chromosomes in the GnomAD database, including 1,488 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 0.12 (1488 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.52
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18462 AN: 152150 Hom.: 1474 Cov.: 33

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0709

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.122 AC: 18514 AN: 152266 Hom.: 1488 Cov.: 33 AF XY: 0.129 AC XY: 9598 AN XY: 74446

African (AFR) AF: 0.131 AC: 5427 AN: 41554

American (AMR) AF: 0.240 AC: 3669 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 431 AN: 3470

East Asian (EAS) AF: 0.239 AC: 1238 AN: 5176

South Asian (SAS) AF: 0.269 AC: 1299 AN: 4824

European-Finnish (FIN) AF: 0.121 AC: 1286 AN: 10608

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0709 AC: 4823 AN: 68028

Other (OTH) AF: 0.141 AC: 297 AN: 2112

Alfa AF: 0.0980 Hom.: 664

Bravo AF: 0.129

Asia WGS AF: 0.298 AC: 1035 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	11
DANN	Benign	0.55
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs4918818; hg19: chr10-115168922;