rs2201217

chr4-45892596-A-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 30 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.00168

Gnomad4 AMR AF: 0.0495

Gnomad4 ASJ AF: 0.00519

Gnomad4 EAS AF: 0.0376

Gnomad4 SAS AF: 0.00621

Gnomad4 FIN AF: 0.0186

Gnomad4 NFE AF: 0.00562

Gnomad4 OTH AF: 0.0128

Alfa AF: 0.0116 Hom.: 1

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2201217; hg19: chr4-45894613;