rs2243210

Variant names:

• chr5-132665694-G-A
• rs2243210

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 0.115 in 152,226 control chromosomes in the GnomAD database, including 1,276 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 0.11 (1276 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17443 AN: 152108 Hom.: 1273 Cov.: 33

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.0352

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.0511

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0776

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.115 AC: 17475 AN: 152226 Hom.: 1276 Cov.: 33 AF XY: 0.114 AC XY: 8496 AN XY: 74434

African (AFR) AF: 0.199 AC: 8278 AN: 41520

American (AMR) AF: 0.119 AC: 1825 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 391 AN: 3468

East Asian (EAS) AF: 0.0355 AC: 184 AN: 5186

South Asian (SAS) AF: 0.137 AC: 658 AN: 4816

European-Finnish (FIN) AF: 0.0511 AC: 542 AN: 10616

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0777 AC: 5283 AN: 68004

Other (OTH) AF: 0.114 AC: 240 AN: 2114

Alfa AF: 0.0969 Hom.: 671

Bravo AF: 0.123

Asia WGS AF: 0.0990 AC: 343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.32
DANN	Benign	0.54
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs2243210; hg19: chr5-132001386;