rs9788716

Positions:

• chr15-47847451-A-C

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 0.0946 in 152,286 control chromosomes in the GnomAD database, including 972 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 0.095 (972 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.131

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.313 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.47847451A>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000259754	ENST00000662551.1	n.188+34535A>C		intron_variant
ENSG00000259754	ENST00000664705.1	n.188+34535A>C		intron_variant
ENSG00000259754	ENST00000665188.1	n.68+34535A>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0946 AC: 14394 AN: 152168 Hom.: 974 Cov.: 32

Gnomad AFR AF: 0.0495

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.0207

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0872

Gnomad OTH AF: 0.0870

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

GnomAD4 genome AF: 0.0946 AC: 14400 AN: 152286 Hom.: 972 Cov.: 32 AF XY: 0.0972 AC XY: 7238 AN XY: 74450

Gnomad4 AFR AF: 0.0495

Gnomad4 AMR AF: 0.135

Gnomad4 ASJ AF: 0.0207

Gnomad4 EAS AF: 0.326

Gnomad4 SAS AF: 0.132

Gnomad4 FIN AF: 0.149

Gnomad4 NFE AF: 0.0872

Gnomad4 OTH AF: 0.0866

Alfa AF: 0.0893 Hom.: 93

Bravo AF: 0.0936

Asia WGS AF: 0.231 AC: 803 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.1
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9788716; hg19: chr15-48139648;