Variant chr12-95999809-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 ENST00000551849.2(ENSG00000257878):n.172-282C>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 0.167 in 152,196 control chromosomes in the GnomAD database, including 2,788 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 0.17 ( 2788 hom., cov: 32)

Consequence

ENST00000551849.2 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0280

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=-0.91).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
LOC102723340	XR_945236.4 linkuse as main transcript	n.571-282C>T	intron_variant, non_coding_transcript_variant
LOC102723340	XR_001749275.3 linkuse as main transcript	n.150-282C>T	intron_variant, non_coding_transcript_variant
LOC102723340	XR_002957424.2 linkuse as main transcript	n.149+3179C>T	intron_variant, non_coding_transcript_variant
LOC102723340	XR_945237.4 linkuse as main transcript	n.247-282C>T	intron_variant, non_coding_transcript_variant

Ensembl

Transcript	HGVSc	Effect	TSL
ENST00000551849.2 linkuse as main transcript	n.172-282C>T	intron_variant, non_coding_transcript_variant	3
ENST00000684881.2 linkuse as main transcript	n.154+3179C>T	intron_variant, non_coding_transcript_variant
ENST00000689841.1 linkuse as main transcript	n.265-282C>T	intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.167

AC:

25382

AN:

152078

Hom.:

2788

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0491

Gnomad AMI

AF:

0.210

Gnomad AMR

AF:

0.148

Gnomad ASJ

AF:

0.194

Gnomad EAS

AF:

0.0185

Gnomad SAS

AF:

0.114

Gnomad FIN

AF:

0.165

Gnomad MID

AF:

0.165

Gnomad NFE

AF:

0.257

Gnomad OTH

AF:

0.158

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

GnomAD4 genome

AF:

0.167

AC:

25379

AN:

152196

Hom.:

2788

Cov.:

AF XY:

0.160

AC XY:

11938

AN XY:

74390

show subpopulations

Gnomad4 AFR

AF:

0.0489

Gnomad4 AMR

AF:

0.148

Gnomad4 ASJ

AF:

0.194

Gnomad4 EAS

AF:

0.0185

Gnomad4 SAS

AF:

0.115

Gnomad4 FIN

AF:

0.165

Gnomad4 NFE

AF:

0.257

Gnomad4 OTH

AF:

0.156

Alfa

AF:

0.200

Hom.:

405

Bravo

AF:

0.161

Asia WGS

AF:

0.0610

AC:

213

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

3.1

DANN

Benign

0.46

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