rs2201217

Variant names:

• chr4-45892596-A-C
• rs2201217

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.011 in 152,286 control chromosomes in the GnomAD database, including 30 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 0.011 (30 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.205
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BS1: Variant frequency is greater than expected in population amr. GnomAd4 allele frequency = 0.011 (1677/152286) while in subpopulation AMR AF = 0.0495 (757/15292). AF 95% confidence interval is 0.0466. There are 30 homozygotes in GnomAd4. There are 961 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 30 gene

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: 0.0110 AC: 1678 AN: 152168 Hom.: 30 Cov.: 33

Gnomad AFR AF: 0.00169

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0495

Gnomad ASJ AF: 0.00519

Gnomad EAS AF: 0.0379

Gnomad SAS AF: 0.00600

Gnomad FIN AF: 0.0186

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00562

Gnomad OTH AF: 0.0134

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

GnomAD4 genome AF: 0.0110 AC: 1677 AN: 152286 Hom.: 30 Cov.: 33 AF XY: 0.0129 AC XY: 961 AN XY: 74448

African (AFR) AF: 0.00168 AC: 70 AN: 41590

American (AMR) AF: 0.0495 AC: 757 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.00519 AC: 18 AN: 3470

East Asian (EAS) AF: 0.0376 AC: 195 AN: 5180

South Asian (SAS) AF: 0.00621 AC: 30 AN: 4832

European-Finnish (FIN) AF: 0.0186 AC: 198 AN: 10620

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00562 AC: 382 AN: 67984

Other (OTH) AF: 0.0128 AC: 27 AN: 2114

Alfa AF: 0.0108 Hom.: 3

Bravo AF: 0.0123

Asia WGS AF: 0.0220 AC: 77 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.1
DANN	Benign	0.42
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs2201217; hg19: chr4-45894613;