rs2018488

Positions:

• chr22-35395781-T-C

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;