16-23206081-C-T

Variant names:

• chr16-23206081-C-T
• rs4401050
• NM_001039.4:c.1078-3669C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001039.4(SCNN1G):​c.1078-3669C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 152,168 control chromosomes in the GnomAD database, including 2,775 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 0.18 (2775 hom., cov: 32)
• Consequence: SCNN1G NM_001039.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.61

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]

ENSG00000260741 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SCNN1G	NM_001039.4	c.1078-3669C>T		intron_variant	Intron 6 of 12	ENST00000300061.3	NP_001030.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCNN1G	ENST00000300061.3	c.1078-3669C>T		intron_variant	Intron 6 of 12	1	NM_001039.4	ENSP00000300061.2
ENSG00000260741	ENST00000563471.1	n.101+6923G>A		intron_variant	Intron 1 of 3	2

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27877 AN: 152050 Hom.: 2766 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.0986

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.190

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.183 AC: 27912 AN: 152168 Hom.: 2775 Cov.: 32 AF XY: 0.182 AC XY: 13509 AN XY: 74364

African (AFR) AF: 0.119 AC: 4943 AN: 41528

American (AMR) AF: 0.243 AC: 3713 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.191 AC: 662 AN: 3470

East Asian (EAS) AF: 0.0986 AC: 511 AN: 5182

South Asian (SAS) AF: 0.250 AC: 1202 AN: 4816

European-Finnish (FIN) AF: 0.194 AC: 2046 AN: 10572

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.207 AC: 14080 AN: 68002

Other (OTH) AF: 0.188 AC: 398 AN: 2112

Alfa AF: 0.186 Hom.: 1698

Bravo AF: 0.187

Asia WGS AF: 0.171 AC: 591 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.12
DANN	Benign	0.49
PhyloP100		-4.6
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4401050; hg19: chr16-23217402;