rs2194225

chr5-35883702-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 0.447 in 151,982 control chromosomes in the GnomAD database, including 16,297 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 0.45 (16297 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.293

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.605 is higher than 0.05.

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: 0.447 AC: 67957 AN: 151864 Hom.: 16296 Cov.: 32

Gnomad AFR AF: 0.612

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.452

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

GnomAD4 genome AF: 0.447 AC: 67974 AN: 151982 Hom.: 16297 Cov.: 32 AF XY: 0.441 AC XY: 32729 AN XY: 74272

Gnomad4 AFR AF: 0.611

Gnomad4 AMR AF: 0.380

Gnomad4 ASJ AF: 0.394

Gnomad4 EAS AF: 0.219

Gnomad4 SAS AF: 0.267

Gnomad4 FIN AF: 0.386

Gnomad4 NFE AF: 0.404

Gnomad4 OTH AF: 0.446

Alfa AF: 0.415 Hom.: 17689

Bravo AF: 0.458

Asia WGS AF: 0.275 AC: 955 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	2.6
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2194225; hg19: chr5-35883804;