rs2243307

Variant names:

• chr5-132672580-G-A
• rs2243307

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The variant allele was found at a frequency of 0.00515 in 137,730 control chromosomes in the GnomAD database, including 37 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 0.0051 (37 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.56
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.09).
• BS2: High Homozygotes in GnomAd4 at 37 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: 0.00515 AC: 709 AN: 137608 Hom.: 37 Cov.: 25

Gnomad AFR AF: 0.00165

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00377

Gnomad ASJ AF: 0.000329

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000975

Gnomad FIN AF: 0.00235

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00932

Gnomad OTH AF: 0.00275

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

GnomAD4 genome AF: 0.00515 AC: 709 AN: 137730 Hom.: 37 Cov.: 25 AF XY: 0.00475 AC XY: 319 AN XY: 67174

African (AFR) AF: 0.00164 AC: 65 AN: 39580

American (AMR) AF: 0.00377 AC: 52 AN: 13804

Ashkenazi Jewish (ASJ) AF: 0.000329 AC: 1 AN: 3044

East Asian (EAS) AF: 0.00 AC: 0 AN: 4884

South Asian (SAS) AF: 0.000976 AC: 4 AN: 4100

European-Finnish (FIN) AF: 0.00235 AC: 22 AN: 9360

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 202

European-Non Finnish (NFE) AF: 0.00932 AC: 560 AN: 60098

Other (OTH) AF: 0.00272 AC: 5 AN: 1836

Alfa AF: 0.00563 Hom.: 5

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.56
DANN	Benign	0.66
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs2243307; hg19: chr5-132008272;