rs4800370

Variant names:

• chr18-22207043-T-A
• rs4800370

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 0.38 in 151,954 control chromosomes in the GnomAD database, including 11,076 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 0.38 (11076 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0210
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.394 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: 0.380 AC: 57750 AN: 151836 Hom.: 11068 Cov.: 32

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.199

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.380 AC: 57784 AN: 151954 Hom.: 11076 Cov.: 32 AF XY: 0.373 AC XY: 27732 AN XY: 74282

African (AFR) AF: 0.390 AC: 16134 AN: 41410

American (AMR) AF: 0.346 AC: 5283 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.419 AC: 1454 AN: 3470

East Asian (EAS) AF: 0.237 AC: 1223 AN: 5152

South Asian (SAS) AF: 0.358 AC: 1727 AN: 4822

European-Finnish (FIN) AF: 0.365 AC: 3846 AN: 10536

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.398 AC: 27032 AN: 67964

Other (OTH) AF: 0.375 AC: 791 AN: 2110

Alfa AF: 0.395 Hom.: 1473

Bravo AF: 0.382

Asia WGS AF: 0.277 AC: 960 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.8
DANN	Benign	0.67
PhyloP100		0.021

Splicing

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

Other links and lift over

dbSNP: rs4800370; hg19: chr18-19787006;