Variant 10-116750088-C-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000437011.1(RPL5P27):n.184C>T variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.766 in 387,742 control chromosomes in the GnomAD database, including 118,636 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 0.71 ( 40921 hom., cov: 32)

Exomes 𝑓: 0.80 ( 77715 hom. )

Consequence

RPL5P27
ENST00000437011.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.78

Variant links:

Genes affected

RPL5P27 (HGNC:36172): (ribosomal protein L5 pseudogene 27)

RPL5P27 links:

HSPA12A (HGNC:19022): (heat shock protein family A (Hsp70) member 12A) Predicted to enable ATP binding activity. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

HSPA12A 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=-0.56).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.841 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Protein
HSPA12A	NM_001330164.2 linkuse as main transcript	c.92-42803G>A	intron_variant	NP_001317093.1
HSPA12A	XM_005269673.6 linkuse as main transcript	c.89-42803G>A	intron_variant	XP_005269730.1
HSPA12A	XM_011539579.3 linkuse as main transcript	c.89-42803G>A	intron_variant	XP_011537881.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RPL5P27	ENST00000437011.1 linkuse as main transcript	n.184C>T		non_coding_transcript_exon_variant	1/2

Frequencies

GnomAD3 genomes

AF:

0.706

AC:

107275

AN:

151980

Hom.:

40919

Cov.:

show subpopulations

Gnomad AFR

AF:

0.388

Gnomad AMI

AF:

0.948

Gnomad AMR

AF:

0.748

Gnomad ASJ

AF:

0.818

Gnomad EAS

AF:

0.610

Gnomad SAS

AF:

0.855

Gnomad FIN

AF:

0.892

Gnomad MID

AF:

0.823

Gnomad NFE

AF:

0.847

Gnomad OTH

AF:

0.727

GnomAD4 exome

AF:

0.804

AC:

189527

AN:

235644

Hom.:

77715

Cov.:

AF XY:

0.809

AC XY:

102056

AN XY:

126114

show subpopulations

Gnomad4 AFR exome

AF:

0.384

Gnomad4 AMR exome

AF:

0.754

Gnomad4 ASJ exome

AF:

0.831

Gnomad4 EAS exome

AF:

0.597

Gnomad4 SAS exome

AF:

0.857

Gnomad4 FIN exome

AF:

0.881

Gnomad4 NFE exome

AF:

0.843

Gnomad4 OTH exome

AF:

0.796

GnomAD4 genome

AF:

0.705

AC:

107299

AN:

152098

Hom.:

40921

Cov.:

AF XY:

0.711

AC XY:

52836

AN XY:

74348

show subpopulations

Gnomad4 AFR

AF:

0.388

Gnomad4 AMR

AF:

0.748

Gnomad4 ASJ

AF:

0.818

Gnomad4 EAS

AF:

0.609

Gnomad4 SAS

AF:

0.855

Gnomad4 FIN

AF:

0.892

Gnomad4 NFE

AF:

0.847

Gnomad4 OTH

AF:

0.727

Alfa

AF:

0.807

Hom.:

28577

Bravo

AF:

0.674

Asia WGS

AF:

0.692

AC:

2406

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.56

CADD

Benign

1.4

DANN

Benign

0.53

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