Variant 5-52136835-G-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The XR_948317.2(LOC105378961):n.321-361G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.316 in 152,020 control chromosomes in the GnomAD database, including 8,414 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 0.32 ( 8414 hom., cov: 32)

Consequence

LOC105378961
XR_948317.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.293

Variant links:

Genes affected

LOC105378961 (HGNC:):

LOC105378961 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=-0.84).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.571 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105378961	XR_948317.2 link	n.321-361G>T		intron_variant
LOC105378961	XR_948318.2 link	n.218-361G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.316

AC:

48008

AN:

151902

Hom.:

8406

Cov.:

show subpopulations

Gnomad AFR

AF:

0.182

Gnomad AMI

AF:

0.318

Gnomad AMR

AF:

0.370

Gnomad ASJ

AF:

0.259

Gnomad EAS

AF:

0.589

Gnomad SAS

AF:

0.397

Gnomad FIN

AF:

0.349

Gnomad MID

AF:

0.207

Gnomad NFE

AF:

0.358

Gnomad OTH

AF:

0.298

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

GnomAD4 genome

AF:

0.316

AC:

48026

AN:

152020

Hom.:

8414

Cov.:

AF XY:

0.318

AC XY:

23615

AN XY:

74322

show subpopulations

Gnomad4 AFR

AF:

0.181

Gnomad4 AMR

AF:

0.371

Gnomad4 ASJ

AF:

0.259

Gnomad4 EAS

AF:

0.588

Gnomad4 SAS

AF:

0.399

Gnomad4 FIN

AF:

0.349

Gnomad4 NFE

AF:

0.358

Gnomad4 OTH

AF:

0.300

Alfa

AF:

0.347

Hom.:

12452

Bravo

AF:

0.314

Asia WGS

AF:

0.457

AC:

1589

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

2.6

DANN

Benign

0.39

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