XM_017023525.2:c.49+18492C>G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS1

The XM_017023525.2(SCNN1B):​c.49+18492C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000385 in 153,324 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00038 ( 1 hom., cov: 31)
Exomes 𝑓: 0.00097 ( 0 hom. )

Consequence

SCNN1B
XM_017023525.2 intron

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:3

Conservation

PhyloP100: -0.723
Variant links:
Genes affected
SCNN1B (HGNC:10600): (sodium channel epithelial 1 subunit beta) Nonvoltage-gated, amiloride-sensitive, sodium channels control fluid and electrolyte transport across epithelia in many organs. These channels are heteromeric complexes consisting of 3 subunits: alpha, beta, and gamma. This gene encodes the beta subunit, and mutations in this gene have been associated with pseudohypoaldosteronism type 1 (PHA1), and Liddle syndrome. [provided by RefSeq, Apr 2009]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
Variant 16-23302296-C-G is Benign according to our data. Variant chr16-23302296-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 318400.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.000381 (58/152290) while in subpopulation EAS AF= 0.00719 (37/5148). AF 95% confidence interval is 0.00536. There are 1 homozygotes in gnomad4. There are 33 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SCNN1BXM_017023525.2 linkc.49+18492C>G intron_variant Intron 2 of 13 XP_016879014.1
SCNN1BNM_000336.3 linkc.-150C>G upstream_gene_variant ENST00000343070.7 NP_000327.2 P51168-1B2R812
SCNN1BNM_001410900.1 linkc.-150C>G upstream_gene_variant NP_001397829.1
SCNN1BXM_011545913.3 linkc.-142C>G upstream_gene_variant XP_011544215.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SCNN1BENST00000569789.1 linkn.178+18492C>G intron_variant Intron 2 of 3 4
SCNN1BENST00000343070.7 linkc.-150C>G upstream_gene_variant 1 NM_000336.3 ENSP00000345751.2 P51168-1

Frequencies

GnomAD3 genomes
AF:
0.000388
AC:
59
AN:
152172
Hom.:
1
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0000724
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00717
Gnomad SAS
AF:
0.00103
Gnomad FIN
AF:
0.000188
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000162
Gnomad OTH
AF:
0.000478
GnomAD4 exome
AF:
0.000967
AC:
1
AN:
1034
Hom.:
0
Cov.:
0
AF XY:
0.00163
AC XY:
1
AN XY:
614
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00476
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.000381
AC:
58
AN:
152290
Hom.:
1
Cov.:
31
AF XY:
0.000443
AC XY:
33
AN XY:
74452
show subpopulations
Gnomad4 AFR
AF:
0.0000722
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00719
Gnomad4 SAS
AF:
0.000828
Gnomad4 FIN
AF:
0.000188
Gnomad4 NFE
AF:
0.000162
Gnomad4 OTH
AF:
0.000473
Alfa
AF:
0.000318
Hom.:
0
Bravo
AF:
0.000234
Asia WGS
AF:
0.00636
AC:
22
AN:
3476

ClinVar

Significance: Likely benign
Submissions summary: Benign:3
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Pseudohypoaldosteronism, type IB1, autosomal recessive Benign:1
Jun 14, 2016
Illumina Laboratory Services, Illumina
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Liddle syndrome 1 Benign:1
Jun 14, 2016
Illumina Laboratory Services, Illumina
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Bronchiectasis with or without elevated sweat chloride 1 Benign:1
Jun 14, 2016
Illumina Laboratory Services, Illumina
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
7.8
DANN
Benign
0.70

Splicing

Name
Calibrated prediction
Score
Prediction
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.

Other links and lift over

dbSNP: rs530631658; hg19: chr16-23313617; API