10-5289196-A-G

Position:

• chr10-5289196-A-G

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 0.636 in 152,144 control chromosomes in the GnomAD database, including 31,130 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 0.64 (31130 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.190

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.743 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.5289196A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.636 AC: 96738 AN: 152026 Hom.: 31098 Cov.: 33

Gnomad AFR AF: 0.696

Gnomad AMI AF: 0.688

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.765

Gnomad FIN AF: 0.603

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.602

Gnomad OTH AF: 0.610

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

GnomAD4 genome AF: 0.636 AC: 96827 AN: 152144 Hom.: 31130 Cov.: 33 AF XY: 0.639 AC XY: 47534 AN XY: 74380

Gnomad4 AFR AF: 0.696

Gnomad4 AMR AF: 0.577

Gnomad4 ASJ AF: 0.601

Gnomad4 EAS AF: 0.756

Gnomad4 SAS AF: 0.763

Gnomad4 FIN AF: 0.603

Gnomad4 NFE AF: 0.602

Gnomad4 OTH AF: 0.610

Alfa AF: 0.619 Hom.: 12974

Bravo AF: 0.633

Asia WGS AF: 0.770 AC: 2678 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	3.0
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2398236; hg19: chr10-5331159;