15-46450130-G-T

Position:

• chr15-46450130-G-T

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 0.946 in 150,460 control chromosomes in the GnomAD database, including 67,776 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 0.95 (67776 hom., cov: 25)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.523

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.984 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.46450130G>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000287704	ENST00000661853.1	n.45+39777G>T		intron_variant
ENSG00000287704	ENST00000686120.1	n.56+39777G>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.947 AC: 142311 AN: 150350 Hom.: 67733 Cov.: 25

Gnomad AFR AF: 0.832

Gnomad AMI AF: 0.985

Gnomad AMR AF: 0.981

Gnomad ASJ AF: 0.983

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.989

Gnomad FIN AF: 0.998

Gnomad MID AF: 0.987

Gnomad NFE AF: 0.991

Gnomad OTH AF: 0.961

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

GnomAD4 genome AF: 0.946 AC: 142407 AN: 150460 Hom.: 67776 Cov.: 25 AF XY: 0.948 AC XY: 69615 AN XY: 73406

Gnomad4 AFR AF: 0.832

Gnomad4 AMR AF: 0.981

Gnomad4 ASJ AF: 0.983

Gnomad4 EAS AF: 0.994

Gnomad4 SAS AF: 0.989

Gnomad4 FIN AF: 0.998

Gnomad4 NFE AF: 0.991

Gnomad4 OTH AF: 0.962

Alfa AF: 0.963 Hom.: 10219

Bravo AF: 0.939

Asia WGS AF: 0.982 AC: 3411 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.63
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs165033; hg19: chr15-46742328;