rs7404408

Variant summary

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

The NM_001039.4(SCNN1G):​c.-44-811C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 152,068 control chromosomes in the GnomAD database, including 3,909 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 0.22 ( 3909 hom., cov: 32)

Consequence

SCNN1G
NM_001039.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.45
Variant links:
Genes affected
SCNN1G (HGNC:10602): (sodium channel epithelial 1 subunit gamma) 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 gamma subunit, and mutations in this gene have been associated with Liddle syndrome. [provided by RefSeq, Apr 2009]

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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=-0.9).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.305 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SCNN1GNM_001039.4 linkuse as main transcriptc.-44-811C>T intron_variant ENST00000300061.3 NP_001030.2 P51170A5X2V1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SCNN1GENST00000300061.3 linkuse as main transcriptc.-44-811C>T intron_variant 1 NM_001039.4 ENSP00000300061.2 P51170
ENSG00000285613ENST00000648673.1 linkuse as main transcriptn.193+786G>A intron_variant

Frequencies

GnomAD3 genomes
AF:
0.217
AC:
32953
AN:
151948
Hom.:
3889
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.135
Gnomad AMI
AF:
0.291
Gnomad AMR
AF:
0.311
Gnomad ASJ
AF:
0.248
Gnomad EAS
AF:
0.160
Gnomad SAS
AF:
0.229
Gnomad FIN
AF:
0.242
Gnomad MID
AF:
0.247
Gnomad NFE
AF:
0.242
Gnomad OTH
AF:
0.222
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.217
AC:
33012
AN:
152068
Hom.:
3909
Cov.:
32
AF XY:
0.217
AC XY:
16135
AN XY:
74338
show subpopulations
Gnomad4 AFR
AF:
0.135
Gnomad4 AMR
AF:
0.312
Gnomad4 ASJ
AF:
0.248
Gnomad4 EAS
AF:
0.160
Gnomad4 SAS
AF:
0.231
Gnomad4 FIN
AF:
0.242
Gnomad4 NFE
AF:
0.242
Gnomad4 OTH
AF:
0.220
Alfa
AF:
0.228
Hom.:
763
Bravo
AF:
0.221
Asia WGS
AF:
0.216
AC:
749
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.087
DANN
Benign
0.28

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: rs7404408; hg19: chr16-23196738; API