rs2018488

Variant names:

• chr22-35395781-T-C
• rs2018488

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 0.0424 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0253 AC: 1048 AN: 41368

American (AMR) AF: 0.0311 AC: 472 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.0191 AC: 66 AN: 3464

East Asian (EAS) AF: 0.00388 AC: 20 AN: 5160

South Asian (SAS) AF: 0.0263 AC: 126 AN: 4798

European-Finnish (FIN) AF: 0.0538 AC: 568 AN: 10552

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0596 AC: 4048 AN: 67952

Other (OTH) AF: 0.0380 AC: 80 AN: 2104

Alfa AF: 0.0537 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
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs2018488; hg19: chr22-35791774;