Variant chr15-47921350-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.189-71359C>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 0.975 in 152,226 control chromosomes in the GnomAD database, including 72,555 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 0.97 ( 72555 hom., cov: 33)

Consequence

ENST00000662551.1 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.66

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=-1.0).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.98 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
LOC124900354	XR_001751516.3 linkuse as main transcript	n.142+36846C>T	intron_variant, non_coding_transcript_variant
LOC124900354	XR_001751517.2 linkuse as main transcript	n.142+36846C>T	intron_variant, non_coding_transcript_variant
LOC124900354	XR_001751518.3 linkuse as main transcript	n.82+5988C>T	intron_variant, non_coding_transcript_variant
LOC124900354	XR_007064618.1 linkuse as main transcript	n.143-28006C>T	intron_variant, non_coding_transcript_variant

Ensembl

Transcript	HGVSc	Effect	TSL
ENST00000662551.1 linkuse as main transcript	n.189-71359C>T	intron_variant, non_coding_transcript_variant
ENST00000560900.1 linkuse as main transcript	n.195+36846C>T	intron_variant, non_coding_transcript_variant	4
ENST00000664705.1 linkuse as main transcript	n.189-71359C>T	intron_variant, non_coding_transcript_variant
ENST00000665188.1 linkuse as main transcript	n.69-71359C>T	intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.975

AC:

148259

AN:

152102

Hom.:

72496

Cov.:

show subpopulations

Gnomad AFR

AF:

0.987

Gnomad AMI

AF:

0.988

Gnomad AMR

AF:

0.961

Gnomad ASJ

AF:

0.979

Gnomad EAS

AF:

0.725

Gnomad SAS

AF:

0.979

Gnomad FIN

AF:

0.986

Gnomad MID

AF:

0.987

Gnomad NFE

AF:

0.986

Gnomad OTH

AF:

0.974

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

GnomAD4 genome

AF:

0.975

AC:

148380

AN:

152226

Hom.:

72555

Cov.:

AF XY:

0.973

AC XY:

72421

AN XY:

74422

show subpopulations

Gnomad4 AFR

AF:

0.987

Gnomad4 AMR

AF:

0.961

Gnomad4 ASJ

AF:

0.979

Gnomad4 EAS

AF:

0.725

Gnomad4 SAS

AF:

0.979

Gnomad4 FIN

AF:

0.986

Gnomad4 NFE

AF:

0.986

Gnomad4 OTH

AF:

0.974

Alfa

AF:

0.984

Hom.:

9296

Bravo

AF:

0.972

Asia WGS

AF:

0.892

AC:

3092

AN:

3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.040

DANN

Benign

0.68

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