rs10866713

Positions:

• chr5-159491886-G-A

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 0.162 in 152,208 control chromosomes in the GnomAD database, including 2,136 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 0.16 (2136 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.215

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.193 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.159491886G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000249738	ENST00000636261.1	n.368-65618G>A		intron_variant		4
ENSG00000283413	ENST00000637629.1	n.104-3593C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24623 AN: 152090 Hom.: 2136 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.00192

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.162 AC: 24625 AN: 152208 Hom.: 2136 Cov.: 32 AF XY: 0.155 AC XY: 11548 AN XY: 74426

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.220

Gnomad4 EAS AF: 0.00193

Gnomad4 SAS AF: 0.143

Gnomad4 FIN AF: 0.120

Gnomad4 NFE AF: 0.195

Gnomad4 OTH AF: 0.163

Alfa AF: 0.185 Hom.: 1440

Bravo AF: 0.164

Asia WGS AF: 0.0660 AC: 230 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.83
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10866713; hg19: chr5-158918894;