rs4800353

Positions:

• chr18-22074176-A-G
• chr18-22074176-A-T

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 0.292 in 152,120 control chromosomes in the GnomAD database, including 9,680 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 0.29 (9680 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.234

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.591 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44265 AN: 152002 Hom.: 9643 Cov.: 32

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.292 AC: 44352 AN: 152120 Hom.: 9680 Cov.: 32 AF XY: 0.291 AC XY: 21625 AN XY: 74362

Gnomad4 AFR AF: 0.597

Gnomad4 AMR AF: 0.346

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.257

Gnomad4 SAS AF: 0.223

Gnomad4 FIN AF: 0.148

Gnomad4 NFE AF: 0.135

Gnomad4 OTH AF: 0.269

Alfa AF: 0.160 Hom.: 5167

Bravo AF: 0.320

Asia WGS AF: 0.282 AC: 980 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.5
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4800353; hg19: chr18-19654137;