Variant chr15-47915269-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000662551.1(ENSG00000259754):n.189-77440C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 151,874 control chromosomes in the GnomAD database, including 2,081 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 0.16 ( 2081 hom., cov: 31)

Consequence

ENST00000662551.1 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.298

Variant links:

Genes affected

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.175 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
LOC124900354	XR_001751516.3 linkuse as main transcript	n.142+30765C>T	intron_variant, non_coding_transcript_variant
LOC124900354	XR_001751517.2 linkuse as main transcript	n.142+30765C>T	intron_variant, non_coding_transcript_variant
LOC124900354	XR_007064618.1 linkuse as main transcript	n.142+30765C>T	intron_variant, non_coding_transcript_variant
LOC124900354	XR_001751518.3 linkuse as main transcript		upstream_gene_variant

Ensembl

Transcript	HGVSc	Effect	TSL
ENST00000662551.1 linkuse as main transcript	n.189-77440C>T	intron_variant, non_coding_transcript_variant
ENST00000560900.1 linkuse as main transcript	n.195+30765C>T	intron_variant, non_coding_transcript_variant	4
ENST00000664705.1 linkuse as main transcript	n.189-77440C>T	intron_variant, non_coding_transcript_variant
ENST00000665188.1 linkuse as main transcript	n.69-77440C>T	intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.159

AC:

24189

AN:

151752

Hom.:

2079

Cov.:

show subpopulations

Gnomad AFR

AF:

0.117

Gnomad AMI

AF:

0.216

Gnomad AMR

AF:

0.163

Gnomad ASJ

AF:

0.223

Gnomad EAS

AF:

0.163

Gnomad SAS

AF:

0.181

Gnomad FIN

AF:

0.157

Gnomad MID

AF:

0.297

Gnomad NFE

AF:

0.178

Gnomad OTH

AF:

0.185

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

GnomAD4 genome

AF:

0.159

AC:

24203

AN:

151874

Hom.:

2081

Cov.:

AF XY:

0.160

AC XY:

11852

AN XY:

74224

show subpopulations

Gnomad4 AFR

AF:

0.117

Gnomad4 AMR

AF:

0.163

Gnomad4 ASJ

AF:

0.223

Gnomad4 EAS

AF:

0.163

Gnomad4 SAS

AF:

0.181

Gnomad4 FIN

AF:

0.157

Gnomad4 NFE

AF:

0.178

Gnomad4 OTH

AF:

0.186

Alfa

AF:

0.183

Hom.:

5332

Bravo

AF:

0.160

Asia WGS

AF:

0.182

AC:

629

AN:

3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

8.1

DANN

Benign

0.67

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over