Variant 15-47886049-T-A details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000662551.1(ENSG00000259754):n.188+73133T>A 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 0.128 in 152,088 control chromosomes in the GnomAD database, including 1,761 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 ( 1761 hom., cov: 32)

Consequence

ENST00000662551.1 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.532

Variant links:

Genes affected

(HGNC:):

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=-0.81).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.332 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
LOC124900354	XR_001751516.3 linkuse as main transcript	n.142+1545T>A	intron_variant, non_coding_transcript_variant
LOC124900354	XR_001751517.2 linkuse as main transcript	n.142+1545T>A	intron_variant, non_coding_transcript_variant
LOC124900354	XR_007064618.1 linkuse as main transcript	n.142+1545T>A	intron_variant, non_coding_transcript_variant

Ensembl

Transcript	HGVSc	Effect	TSL
ENST00000662551.1 linkuse as main transcript	n.188+73133T>A	intron_variant, non_coding_transcript_variant
ENST00000560900.1 linkuse as main transcript	n.195+1545T>A	intron_variant, non_coding_transcript_variant	4
ENST00000664705.1 linkuse as main transcript	n.188+73133T>A	intron_variant, non_coding_transcript_variant
ENST00000665188.1 linkuse as main transcript	n.68+73133T>A	intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.127

AC:

19363

AN:

151970

Hom.:

1750

Cov.:

show subpopulations

Gnomad AFR

AF:

0.192

Gnomad AMI

AF:

0.182

Gnomad AMR

AF:

0.160

Gnomad ASJ

AF:

0.0360

Gnomad EAS

AF:

0.346

Gnomad SAS

AF:

0.276

Gnomad FIN

AF:

0.0709

Gnomad MID

AF:

0.0573

Gnomad NFE

AF:

0.0674

Gnomad OTH

AF:

0.104

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

GnomAD4 genome

AF:

0.128

AC:

19415

AN:

152088

Hom.:

1761

Cov.:

AF XY:

0.131

AC XY:

9740

AN XY:

74350

show subpopulations

Gnomad4 AFR

AF:

0.193

Gnomad4 AMR

AF:

0.161

Gnomad4 ASJ

AF:

0.0360

Gnomad4 EAS

AF:

0.346

Gnomad4 SAS

AF:

0.275

Gnomad4 FIN

AF:

0.0709

Gnomad4 NFE

AF:

0.0674

Gnomad4 OTH

AF:

0.110

Alfa

AF:

0.0394

Hom.:

Bravo

AF:

0.134

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

0.23

DANN

Benign

0.60

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