Variant 6-145919501-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001042683.3(SHPRH):c.4009-10A>G variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00326 in 1,611,796 control chromosomes in the GnomAD database, including 120 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0043 ( 18 hom., cov: 32)

Exomes 𝑓: 0.0032 ( 102 hom. )

Consequence

SHPRH
NM_001042683.3 splice_polypyrimidine_tract, intron

Scores

Splicing: ADA: 0.00001212

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.695

Variant links:

Genes affected

SHPRH (HGNC:19336): (SNF2 histone linker PHD RING helicase) SHPRH is a ubiquitously expressed protein that contains motifs characteristics of several DNA repair proteins, transcription factors, and helicases. SHPRH is a functional homolog of S. cerevisiae RAD5 (Unk et al., 2006 [PubMed 17108083]).[supplied by OMIM, Mar 2008]

SHPRH links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BP6

Variant 6-145919501-T-C is Benign according to our data. Variant chr6-145919501-T-C is described in ClinVar as [Benign]. Clinvar id is 732848.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0656 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SHPRH	NM_001042683.3 linkuse as main transcript	c.4009-10A>G		splice_polypyrimidine_tract_variant, intron_variant		ENST00000275233.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SHPRH	ENST00000275233.12 linkuse as main transcript	c.4009-10A>G		splice_polypyrimidine_tract_variant, intron_variant		1	NM_001042683.3	P1	Q149N8-1

Frequencies

GnomAD3 genomes

AF:

0.00426

AC:

648

AN:

152078

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000628

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000656

Gnomad ASJ

AF:

0.00202

Gnomad EAS

AF:

0.0713

Gnomad SAS

AF:

0.00828

Gnomad FIN

AF:

0.0139

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000529

Gnomad OTH

AF:

0.00526

GnomAD3 exomes

AF:

0.00851

AC:

2098

AN:

246508

Hom.:

AF XY:

0.00817

AC XY:

1093

AN XY:

133726

show subpopulations

Gnomad AFR exome

AF:

0.000649

Gnomad AMR exome

AF:

0.000234

Gnomad ASJ exome

AF:

0.00191

Gnomad EAS exome

AF:

0.0792

Gnomad SAS exome

AF:

0.00684

Gnomad FIN exome

AF:

0.0143

Gnomad NFE exome

AF:

0.000923

Gnomad OTH exome

AF:

0.00638

GnomAD4 exome

AF:

0.00316

AC:

4606

AN:

1459600

Hom.:

102

Cov.:

AF XY:

0.00323

AC XY:

2347

AN XY:

726062

show subpopulations

Gnomad4 AFR exome

AF:

0.000270

Gnomad4 AMR exome

AF:

0.000180

Gnomad4 ASJ exome

AF:

0.00223

Gnomad4 EAS exome

AF:

0.0641

Gnomad4 SAS exome

AF:

0.00610

Gnomad4 FIN exome

AF:

0.0143

Gnomad4 NFE exome

AF:

0.000366

Gnomad4 OTH exome

AF:

0.00496

GnomAD4 genome

AF:

0.00428

AC:

652

AN:

152196

Hom.:

Cov.:

AF XY:

0.00512

AC XY:

381

AN XY:

74420

show subpopulations

Gnomad4 AFR

AF:

0.000626

Gnomad4 AMR

AF:

0.000656

Gnomad4 ASJ

AF:

0.00202

Gnomad4 EAS

AF:

0.0716

Gnomad4 SAS

AF:

0.00850

Gnomad4 FIN

AF:

0.0139

Gnomad4 NFE

AF:

0.000529

Gnomad4 OTH

AF:

0.00616

Alfa

AF:

0.00106

Hom.:

Bravo

AF:

0.00357

Asia WGS

AF:

0.0460

AC:

161

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jun 27, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

1.6

DANN

Benign

0.57

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000012

dbscSNV1_RF

Benign

0.0

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over