rs2243302

Variant names:

• chr5-132668839-G-A
• rs2243302

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 0.0756 in 152,238 control chromosomes in the GnomAD database, including 539 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 0.076 (539 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.126
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.11 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: 0.0756 AC: 11507 AN: 152120 Hom.: 539 Cov.: 32

Gnomad AFR AF: 0.0213

Gnomad AMI AF: 0.172

Gnomad AMR AF: 0.0980

Gnomad ASJ AF: 0.0822

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0301

Gnomad FIN AF: 0.0625

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.0756 AC: 11505 AN: 152238 Hom.: 539 Cov.: 32 AF XY: 0.0724 AC XY: 5391 AN XY: 74444

African (AFR) AF: 0.0212 AC: 882 AN: 41526

American (AMR) AF: 0.0981 AC: 1500 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0822 AC: 285 AN: 3466

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5190

South Asian (SAS) AF: 0.0303 AC: 146 AN: 4818

European-Finnish (FIN) AF: 0.0625 AC: 664 AN: 10618

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7638 AN: 68002

Other (OTH) AF: 0.0998 AC: 211 AN: 2114

Alfa AF: 0.0588 Hom.: 99

Bravo AF: 0.0762

Asia WGS AF: 0.0140 AC: 49 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.0
DANN	Benign	0.44
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs2243302; hg19: chr5-132004531;