Variant 12-53867976-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 ENST00000663306.1(ENSG00000286069):n.480-7179C>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 0.425 in 151,998 control chromosomes in the GnomAD database, including 14,474 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 0.42 ( 14474 hom., cov: 31)

Consequence

ENST00000663306.1 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.308

Variant links:

Genes affected

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.69).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.557 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
LOC107984525	XR_002957415.2 linkuse as main transcript	n.451+17564C>T	intron_variant, non_coding_transcript_variant
LOC107984525	XR_001749153.2 linkuse as main transcript	n.282-7179C>T	intron_variant, non_coding_transcript_variant
LOC107984525	XR_007063319.1 linkuse as main transcript	n.1401-7179C>T	intron_variant, non_coding_transcript_variant
LOC107984525	XR_007063320.1 linkuse as main transcript	n.229-7179C>T	intron_variant, non_coding_transcript_variant

Ensembl

Transcript	HGVSc	Effect
ENST00000663306.1 linkuse as main transcript	n.480-7179C>T	intron_variant, non_coding_transcript_variant
ENST00000652339.1 linkuse as main transcript	n.509+7098C>T	intron_variant, non_coding_transcript_variant
ENST00000654713.1 linkuse as main transcript	n.317+17564C>T	intron_variant, non_coding_transcript_variant
ENST00000656247.1 linkuse as main transcript	n.344+17564C>T	intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.425

AC:

64506

AN:

151880

Hom.:

14462

Cov.:

show subpopulations

Gnomad AFR

AF:

0.563

Gnomad AMI

AF:

0.404

Gnomad AMR

AF:

0.288

Gnomad ASJ

AF:

0.420

Gnomad EAS

AF:

0.228

Gnomad SAS

AF:

0.359

Gnomad FIN

AF:

0.320

Gnomad MID

AF:

0.320

Gnomad NFE

AF:

0.409

Gnomad OTH

AF:

0.384

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

GnomAD4 genome

AF:

0.425

AC:

64553

AN:

151998

Hom.:

14474

Cov.:

AF XY:

0.415

AC XY:

30857

AN XY:

74290

show subpopulations

Gnomad4 AFR

AF:

0.563

Gnomad4 AMR

AF:

0.288

Gnomad4 ASJ

AF:

0.420

Gnomad4 EAS

AF:

0.228

Gnomad4 SAS

AF:

0.359

Gnomad4 FIN

AF:

0.320

Gnomad4 NFE

AF:

0.409

Gnomad4 OTH

AF:

0.382

Alfa

AF:

0.409

Hom.:

2086

Bravo

AF:

0.426

Asia WGS

AF:

0.300

AC:

1049

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.69

CADD

Benign

4.6

DANN

Benign

0.78

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