Variant chr6-23404048-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The ENST00000658716.1(ENSG00000235743):n.347T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 152,194 control chromosomes in the GnomAD database, including 1,511 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 0.13 ( 1511 hom., cov: 33)

Consequence

ENST00000658716.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.31

Variant links:

Genes affected

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.24).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.218 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons
LOC105374976	XR_001744046.2 linkuse as main transcript	n.481+53542A>G	intron_variant, non_coding_transcript_variant
LOC124900213	XR_007059502.1 linkuse as main transcript	n.1017T>C	non_coding_transcript_exon_variant	6/6
LOC124900213	XR_007059503.1 linkuse as main transcript	n.1000T>C	non_coding_transcript_exon_variant	6/6
LOC105374976	XR_007059501.1 linkuse as main transcript	n.459+53542A>G	intron_variant, non_coding_transcript_variant

Ensembl

Transcript	HGVSc	Effect	#exon/exons
ENST00000658716.1 linkuse as main transcript	n.347T>C	non_coding_transcript_exon_variant	3/3
ENST00000690652.2 linkuse as main transcript	n.291+53542A>G	intron_variant, non_coding_transcript_variant
ENST00000700866.1 linkuse as main transcript	n.262-31919A>G	intron_variant, non_coding_transcript_variant
ENST00000702216.1 linkuse as main transcript	n.284-24680A>G	intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.130

AC:

19731

AN:

152076

Hom.:

1505

Cov.:

show subpopulations

Gnomad AFR

AF:

0.222

Gnomad AMI

AF:

0.0877

Gnomad AMR

AF:

0.0915

Gnomad ASJ

AF:

0.0775

Gnomad EAS

AF:

0.153

Gnomad SAS

AF:

0.0758

Gnomad FIN

AF:

0.106

Gnomad MID

AF:

0.111

Gnomad NFE

AF:

0.0918

Gnomad OTH

AF:

0.118

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

GnomAD4 genome

AF:

0.130

AC:

19767

AN:

152194

Hom.:

1511

Cov.:

AF XY:

0.129

AC XY:

9626

AN XY:

74408

show subpopulations

Gnomad4 AFR

AF:

0.222

Gnomad4 AMR

AF:

0.0914

Gnomad4 ASJ

AF:

0.0775

Gnomad4 EAS

AF:

0.153

Gnomad4 SAS

AF:

0.0752

Gnomad4 FIN

AF:

0.106

Gnomad4 NFE

AF:

0.0917

Gnomad4 OTH

AF:

0.118

Alfa

AF:

0.0983

Hom.:

1124

Bravo

AF:

0.135

Asia WGS

AF:

0.101

AC:

353

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.24

CADD

Benign

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