rs4800370

Variant names:

• chr18-22207043-T-A
• rs4800370

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.380 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

Gnomad4 AFR AF: 0.390

Gnomad4 AMR AF: 0.346

Gnomad4 ASJ AF: 0.419

Gnomad4 EAS AF: 0.237

Gnomad4 SAS AF: 0.358

Gnomad4 FIN AF: 0.365

Gnomad4 NFE AF: 0.398

Gnomad4 OTH AF: 0.375

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4800370; hg19: chr18-19787006;