rs2018488

Variant names:

• chr22-35395781-T-C
• rs2018488

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 0.0424 in 151,800 control chromosomes in the GnomAD database, including 172 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 0.042 (172 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.734

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.058 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: 0.0424 AC: 6426 AN: 151682 Hom.: 172 Cov.: 28

Gnomad AFR AF: 0.0252

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0311

Gnomad ASJ AF: 0.0191

Gnomad EAS AF: 0.00406

Gnomad SAS AF: 0.0260

Gnomad FIN AF: 0.0538

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0596

Gnomad OTH AF: 0.0389

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

GnomAD4 genome AF: 0.0424 AC: 6432 AN: 151800 Hom.: 172 Cov.: 28 AF XY: 0.0414 AC XY: 3073 AN XY: 74176

Gnomad4 AFR AF: 0.0253

Gnomad4 AMR AF: 0.0311

Gnomad4 ASJ AF: 0.0191

Gnomad4 EAS AF: 0.00388

Gnomad4 SAS AF: 0.0263

Gnomad4 FIN AF: 0.0538

Gnomad4 NFE AF: 0.0596

Gnomad4 OTH AF: 0.0380

Alfa AF: 0.0551 Hom.: 32

Bravo AF: 0.0392

Asia WGS AF: 0.0150 AC: 53 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2018488; hg19: chr22-35791774;