15-46450130-G-T

Variant names:

• chr15-46450130-G-T
• rs165033
• ENST00000661853.1:n.45+39777G>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000661853.1(ENSG00000287704):​n.45+39777G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000287704 ENST00000661853.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.523

Genes affected

ENSG00000287704 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287704	ENST00000661853.1	n.45+39777G>T		intron_variant	Intron 1 of 1
ENSG00000287704	ENST00000686120.1	n.56+39777G>T		intron_variant	Intron 1 of 2

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;