chr15-47778678-G-A

Position:

• chr15-47778678-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 0.265 in 152,014 control chromosomes in the GnomAD database, including 5,541 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 0.27 (5541 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.482

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.47778678G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01491	ENST00000558792.6	n.572-4270C>T		intron_variant		3
LINC01491	ENST00000651940.1	n.580-4270C>T		intron_variant
LINC01491	ENST00000653152.1	n.620-4270C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40339 AN: 151896 Hom.: 5539 Cov.: 33

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.265 AC: 40355 AN: 152014 Hom.: 5541 Cov.: 33 AF XY: 0.266 AC XY: 19777 AN XY: 74276

Gnomad4 AFR AF: 0.240

Gnomad4 AMR AF: 0.231

Gnomad4 ASJ AF: 0.335

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.260

Gnomad4 FIN AF: 0.339

Gnomad4 NFE AF: 0.285

Gnomad4 OTH AF: 0.266

Alfa AF: 0.294 Hom.: 1401

Bravo AF: 0.249

Asia WGS AF: 0.241 AC: 838 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	3.8
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11855291; hg19: chr15-48070875;