5-108580035-A-G

Variant names:

• chr5-108580035-A-G
• rs10447248

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 0.688 in 152,076 control chromosomes in the GnomAD database, including 37,381 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 0.69 (37381 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.535
• Publications: 14 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 = 0.853 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: 0.688 AC: 104563 AN: 151956 Hom.: 37326 Cov.: 31

Gnomad AFR AF: 0.860

Gnomad AMI AF: 0.746

Gnomad AMR AF: 0.616

Gnomad ASJ AF: 0.669

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.656

Gnomad OTH AF: 0.671

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

GnomAD4 genome AF: 0.688 AC: 104669 AN: 152076 Hom.: 37381 Cov.: 31 AF XY: 0.680 AC XY: 50533 AN XY: 74310

African (AFR) AF: 0.860 AC: 35713 AN: 41506

American (AMR) AF: 0.615 AC: 9412 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.669 AC: 2321 AN: 3470

East Asian (EAS) AF: 0.315 AC: 1623 AN: 5146

South Asian (SAS) AF: 0.400 AC: 1925 AN: 4808

European-Finnish (FIN) AF: 0.644 AC: 6798 AN: 10558

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.656 AC: 44599 AN: 67980

Other (OTH) AF: 0.668 AC: 1409 AN: 2110

Alfa AF: 0.661 Hom.: 133255

Bravo AF: 0.694

Asia WGS AF: 0.420 AC: 1464 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.84
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs10447248; hg19: chr5-107915736; COSMIC: COSV60180725;