rs175200

Variant names:

• chr22-20180986-G-A
• rs175200

Your query was ambiguous. Multiple possible variants found:

• chr22-20180986-G-A
• chr22-20180986-G-C

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 0.4 in 152,098 control chromosomes in the GnomAD database, including 12,952 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 0.40 (12952 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.675
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.468 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: 0.400 AC: 60825 AN: 151982 Hom.: 12949 Cov.: 33

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.365

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.404

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

GnomAD4 genome AF: 0.400 AC: 60845 AN: 152098 Hom.: 12952 Cov.: 33 AF XY: 0.401 AC XY: 29801 AN XY: 74352

African (AFR) AF: 0.245 AC: 10175 AN: 41492

American (AMR) AF: 0.394 AC: 6025 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.417 AC: 1446 AN: 3470

East Asian (EAS) AF: 0.366 AC: 1890 AN: 5170

South Asian (SAS) AF: 0.437 AC: 2107 AN: 4820

European-Finnish (FIN) AF: 0.547 AC: 5798 AN: 10594

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.472 AC: 32099 AN: 67950

Other (OTH) AF: 0.400 AC: 845 AN: 2110

Alfa AF: 0.425 Hom.: 2464

Bravo AF: 0.381

Asia WGS AF: 0.373 AC: 1296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.7
DANN	Benign	0.50
PhyloP100		0.68

Splicing

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

Other links and lift over

dbSNP: rs175200; hg19: chr22-20168509;