Variant 1-206935822-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000356495.5(PIGR):c.1046-4C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.417 in 1,582,638 control chromosomes in the GnomAD database, including 143,473 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.36 ( 10716 hom., cov: 32)

Exomes 𝑓: 0.42 ( 132757 hom. )

Consequence

PIGR
ENST00000356495.5 splice_region, splice_polypyrimidine_tract, intron

Scores

Splicing: ADA: 0.00003185

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.628

Variant links:

Genes affected

PIGR (HGNC:8968): (polymeric immunoglobulin receptor) This gene is a member of the immunoglobulin superfamily. The encoded poly-Ig receptor binds polymeric immunoglobulin molecules at the basolateral surface of epithelial cells; the complex is then transported across the cell to be secreted at the apical surface. A significant association was found between immunoglobulin A nephropathy and several SNPs in this gene.[provided by RefSeq, Sep 2009]

PIGR links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.75).

BP6

Variant 1-206935822-G-A is Benign according to our data. Variant chr1-206935822-G-A is described in ClinVar as [Benign]. Clinvar id is 1244747.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PIGR	NM_002644.4 linkuse as main transcript	c.1046-4C>T		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		ENST00000356495.5	NP_002635.2
PIGR	XM_011509629.2 linkuse as main transcript	c.1046-4C>T		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant			XP_011507931.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PIGR	ENST00000356495.5 linkuse as main transcript	c.1046-4C>T		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		1	NM_002644.4	ENSP00000348888	P1

Frequencies

GnomAD3 genomes

AF:

0.356

AC:

54097

AN:

151992

Hom.:

10709

Cov.:

show subpopulations

Gnomad AFR

AF:

0.182

Gnomad AMI

AF:

0.499

Gnomad AMR

AF:

0.338

Gnomad ASJ

AF:

0.454

Gnomad EAS

AF:

0.341

Gnomad SAS

AF:

0.231

Gnomad FIN

AF:

0.403

Gnomad MID

AF:

0.522

Gnomad NFE

AF:

0.459

Gnomad OTH

AF:

0.409

GnomAD3 exomes

AF:

0.379

AC:

88109

AN:

232440

Hom.:

17717

AF XY:

0.383

AC XY:

48321

AN XY:

126146

show subpopulations

Gnomad AFR exome

AF:

0.172

Gnomad AMR exome

AF:

0.302

Gnomad ASJ exome

AF:

0.476

Gnomad EAS exome

AF:

0.330

Gnomad SAS exome

AF:

0.254

Gnomad FIN exome

AF:

0.408

Gnomad NFE exome

AF:

0.459

Gnomad OTH exome

AF:

0.426

GnomAD4 exome

AF:

0.424

AC:

606036

AN:

1430528

Hom.:

132757

Cov.:

AF XY:

0.421

AC XY:

297672

AN XY:

707228

show subpopulations

Gnomad4 AFR exome

AF:

0.173

Gnomad4 AMR exome

AF:

0.309

Gnomad4 ASJ exome

AF:

0.471

Gnomad4 EAS exome

AF:

0.293

Gnomad4 SAS exome

AF:

0.254

Gnomad4 FIN exome

AF:

0.413

Gnomad4 NFE exome

AF:

0.453

Gnomad4 OTH exome

AF:

0.418

GnomAD4 genome

AF:

0.356

AC:

54115

AN:

152110

Hom.:

10716

Cov.:

AF XY:

0.349

AC XY:

25984

AN XY:

74376

show subpopulations

Gnomad4 AFR

AF:

0.182

Gnomad4 AMR

AF:

0.337

Gnomad4 ASJ

AF:

0.454

Gnomad4 EAS

AF:

0.340

Gnomad4 SAS

AF:

0.231

Gnomad4 FIN

AF:

0.403

Gnomad4 NFE

AF:

0.459

Gnomad4 OTH

AF:

0.413

Alfa

AF:

0.368

Hom.:

4238

Bravo

AF:

0.346

Asia WGS

AF:

0.277

AC:

964

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 06, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

DANN

Benign

0.87

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000032

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