Variant 10-64688715-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 ENST00000654191.1(ENSG00000228566):n.734-2727T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 151,984 control chromosomes in the GnomAD database, including 3,194 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 0.20 ( 3194 hom., cov: 32)

Consequence

ENSG00000228566
ENST00000654191.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.162

Variant links:

Genes affected

ENSG00000228566 (HGNC:):

ENSG00000228566 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=-0.87).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.331 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
LOC124902439	XR_007062160.1 link	n.713-2727T>C	intron_variant
LOC124902439	XR_007062161.1 link	n.715-2727T>C	intron_variant
LOC124902439	XR_007062165.1 link	n.270-2727T>C	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000228566	ENST00000654191.1 link	n.734-2727T>C		intron_variant
ENSG00000228566	ENST00000660795.1 link	n.580-2727T>C		intron_variant

Frequencies

GnomAD3 genomes

AF:

0.198

AC:

30005

AN:

151866

Hom.:

3178

Cov.:

show subpopulations

Gnomad AFR

AF:

0.224

Gnomad AMI

AF:

0.256

Gnomad AMR

AF:

0.284

Gnomad ASJ

AF:

0.225

Gnomad EAS

AF:

0.345

Gnomad SAS

AF:

0.260

Gnomad FIN

AF:

0.197

Gnomad MID

AF:

0.129

Gnomad NFE

AF:

0.145

Gnomad OTH

AF:

0.179

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

GnomAD4 genome

AF:

0.198

AC:

30041

AN:

151984

Hom.:

3194

Cov.:

AF XY:

0.203

AC XY:

15058

AN XY:

74260

show subpopulations

Gnomad4 AFR

AF:

0.224

Gnomad4 AMR

AF:

0.285

Gnomad4 ASJ

AF:

0.225

Gnomad4 EAS

AF:

0.345

Gnomad4 SAS

AF:

0.259

Gnomad4 FIN

AF:

0.197

Gnomad4 NFE

AF:

0.145

Gnomad4 OTH

AF:

0.181

Alfa

AF:

0.167

Hom.:

2084

Bravo

AF:

0.208

Asia WGS

AF:

0.276

AC:

950

AN:

3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

6.5

DANN

Benign

0.77

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