Variant chr6-23518043-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000690652.2(ENSG00000289368):n.211-60373A>G 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 0.549 in 151,948 control chromosomes in the GnomAD database, including 23,138 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 0.55 ( 23138 hom., cov: 31)

Consequence

ENST00000690652.2 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.124

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=-0.94).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.593 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374976	XR_001744046.2 linkuse as main transcript	n.401-60373A>G		intron_variant, non_coding_transcript_variant
LOC105374976	XR_007059501.1 linkuse as main transcript	n.379-60373A>G		intron_variant, non_coding_transcript_variant

Ensembl

Transcript	HGVSc	Effect
ENST00000690652.2 linkuse as main transcript	n.211-60373A>G	intron_variant, non_coding_transcript_variant
ENST00000700866.1 linkuse as main transcript	n.181-60373A>G	intron_variant, non_coding_transcript_variant
ENST00000702216.1 linkuse as main transcript	n.203-60373A>G	intron_variant, non_coding_transcript_variant
ENST00000702386.1 linkuse as main transcript	n.200-60373A>G	intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.549

AC:

83306

AN:

151830

Hom.:

23105

Cov.:

show subpopulations

Gnomad AFR

AF:

0.599

Gnomad AMI

AF:

0.513

Gnomad AMR

AF:

0.473

Gnomad ASJ

AF:

0.645

Gnomad EAS

AF:

0.339

Gnomad SAS

AF:

0.489

Gnomad FIN

AF:

0.550

Gnomad MID

AF:

0.649

Gnomad NFE

AF:

0.550

Gnomad OTH

AF:

0.540

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

GnomAD4 genome

AF:

0.549

AC:

83394

AN:

151948

Hom.:

23138

Cov.:

AF XY:

0.545

AC XY:

40479

AN XY:

74260

show subpopulations

Gnomad4 AFR

AF:

0.600

Gnomad4 AMR

AF:

0.473

Gnomad4 ASJ

AF:

0.645

Gnomad4 EAS

AF:

0.340

Gnomad4 SAS

AF:

0.488

Gnomad4 FIN

AF:

0.550

Gnomad4 NFE

AF:

0.550

Gnomad4 OTH

AF:

0.545

Alfa

AF:

0.549

Hom.:

5708

Bravo

AF:

0.543

Asia WGS

AF:

0.458

AC:

1593

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

2.6

DANN

Benign

0.59

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