Variant chr12-53867372-A-C 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.480-7783A>C 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 0.678 in 152,122 control chromosomes in the GnomAD database, including 35,606 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 0.68 ( 35606 hom., cov: 32)

Consequence

ENST00000663306.1 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.373

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=-0.8).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.719 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
LOC107984525	XR_002957415.2 linkuse as main transcript	n.451+16960A>C	intron_variant, non_coding_transcript_variant
LOC107984525	XR_001749153.2 linkuse as main transcript	n.282-7783A>C	intron_variant, non_coding_transcript_variant
LOC107984525	XR_007063319.1 linkuse as main transcript	n.1401-7783A>C	intron_variant, non_coding_transcript_variant
LOC107984525	XR_007063320.1 linkuse as main transcript	n.229-7783A>C	intron_variant, non_coding_transcript_variant

Ensembl

Transcript	HGVSc	Effect
ENST00000663306.1 linkuse as main transcript	n.480-7783A>C	intron_variant, non_coding_transcript_variant
ENST00000652339.1 linkuse as main transcript	n.509+6494A>C	intron_variant, non_coding_transcript_variant
ENST00000654713.1 linkuse as main transcript	n.317+16960A>C	intron_variant, non_coding_transcript_variant
ENST00000656247.1 linkuse as main transcript	n.344+16960A>C	intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.679

AC:

103135

AN:

152004

Hom.:

35597

Cov.:

show subpopulations

Gnomad AFR

AF:

0.687

Gnomad AMI

AF:

0.568

Gnomad AMR

AF:

0.544

Gnomad ASJ

AF:

0.677

Gnomad EAS

AF:

0.338

Gnomad SAS

AF:

0.734

Gnomad FIN

AF:

0.703

Gnomad MID

AF:

0.634

Gnomad NFE

AF:

0.724

Gnomad OTH

AF:

0.668

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

GnomAD4 genome

AF:

0.678

AC:

103177

AN:

152122

Hom.:

35606

Cov.:

AF XY:

0.673

AC XY:

50028

AN XY:

74354

show subpopulations

Gnomad4 AFR

AF:

0.686

Gnomad4 AMR

AF:

0.544

Gnomad4 ASJ

AF:

0.677

Gnomad4 EAS

AF:

0.337

Gnomad4 SAS

AF:

0.734

Gnomad4 FIN

AF:

0.703

Gnomad4 NFE

AF:

0.724

Gnomad4 OTH

AF:

0.664

Alfa

AF:

0.703

Hom.:

74729

Bravo

AF:

0.661

Asia WGS

AF:

0.548

AC:

1909

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

DANN

Benign

0.84

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