rs647903

Positions:

• chr15-47798219-G-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 0.543 in 152,006 control chromosomes in the GnomAD database, including 23,195 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 0.54 (23195 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.903

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.11).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.851 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.47798219G>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01491	ENST00000558792.6	n.571+5165C>G		intron_variant		3
LINC01491	ENST00000651940.1	n.435+5165C>G		intron_variant
LINC01491	ENST00000653152.1	n.475+5165C>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.542 AC: 82373 AN: 151888 Hom.: 23154 Cov.: 32

Gnomad AFR AF: 0.638

Gnomad AMI AF: 0.501

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.873

Gnomad SAS AF: 0.599

Gnomad FIN AF: 0.475

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.543 AC: 82481 AN: 152006 Hom.: 23195 Cov.: 32 AF XY: 0.550 AC XY: 40854 AN XY: 74302

Gnomad4 AFR AF: 0.638

Gnomad4 AMR AF: 0.589

Gnomad4 ASJ AF: 0.525

Gnomad4 EAS AF: 0.872

Gnomad4 SAS AF: 0.599

Gnomad4 FIN AF: 0.475

Gnomad4 NFE AF: 0.456

Gnomad4 OTH AF: 0.573

Alfa AF: 0.493 Hom.: 2347

Bravo AF: 0.555

Asia WGS AF: 0.726 AC: 2517 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.41
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs647903; hg19: chr15-48090416;