Variant 10-18714164-G-A details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000654305.1(ENSG00000234244):n.93+3803G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.563 in 151,872 control chromosomes in the GnomAD database, including 24,860 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 0.56 ( 24860 hom., cov: 31)

Consequence

ENSG00000234244
ENST00000654305.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.272

Variant links:

Genes affected

ENSG00000234244 (HGNC:):

ENSG00000234244 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=-0.97).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.71 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105376440	XR_930720.2 link	n.51+3803G>A		intron_variant
LOC105376440	XR_930721.2 link	n.68+3803G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000234244	ENST00000654305.1 link	n.93+3803G>A		intron_variant
ENSG00000234244	ENST00000654415.1 link	n.78+3803G>A		intron_variant

Frequencies

GnomAD3 genomes

AF:

0.563

AC:

85472

AN:

151754

Hom.:

24823

Cov.:

show subpopulations

Gnomad AFR

AF:

0.717

Gnomad AMI

AF:

0.722

Gnomad AMR

AF:

0.543

Gnomad ASJ

AF:

0.441

Gnomad EAS

AF:

0.549

Gnomad SAS

AF:

0.377

Gnomad FIN

AF:

0.478

Gnomad MID

AF:

0.389

Gnomad NFE

AF:

0.508

Gnomad OTH

AF:

0.519

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

GnomAD4 genome

AF:

0.563

AC:

85559

AN:

151872

Hom.:

24860

Cov.:

AF XY:

0.557

AC XY:

41358

AN XY:

74230

show subpopulations

Gnomad4 AFR

AF:

0.717

Gnomad4 AMR

AF:

0.543

Gnomad4 ASJ

AF:

0.441

Gnomad4 EAS

AF:

0.549

Gnomad4 SAS

AF:

0.376

Gnomad4 FIN

AF:

0.478

Gnomad4 NFE

AF:

0.508

Gnomad4 OTH

AF:

0.513

Alfa

AF:

0.503

Hom.:

38783

Bravo

AF:

0.582

Asia WGS

AF:

0.477

AC:

1659

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

8.2

DANN

Benign

0.65

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