rs11074553

chr16-23199998-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001039.4(SCNN1G):c.1077+2571G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.547 in 151,920 control chromosomes in the GnomAD database, including 23,617 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 0.55 (23617 hom., cov: 31)
• Consequence: SCNN1G NM_001039.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.46

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.798 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SCNN1G	NM_001039.4	c.1077+2571G>A		intron_variant		ENST00000300061.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SCNN1G	ENST00000300061.3	c.1077+2571G>A		intron_variant		1	NM_001039.4	P1
	ENST00000563471.1	n.102-3451C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.547 AC: 83063 AN: 151804 Hom.: 23607 Cov.: 31

Gnomad AFR AF: 0.417

Gnomad AMI AF: 0.609

Gnomad AMR AF: 0.669

Gnomad ASJ AF: 0.642

Gnomad EAS AF: 0.818

Gnomad SAS AF: 0.775

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.561

Gnomad OTH AF: 0.585

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

GnomAD4 genome AF: 0.547 AC: 83106 AN: 151920 Hom.: 23617 Cov.: 31 AF XY: 0.550 AC XY: 40860 AN XY: 74234

Gnomad4 AFR AF: 0.416

Gnomad4 AMR AF: 0.669

Gnomad4 ASJ AF: 0.642

Gnomad4 EAS AF: 0.818

Gnomad4 SAS AF: 0.776

Gnomad4 FIN AF: 0.511

Gnomad4 NFE AF: 0.561

Gnomad4 OTH AF: 0.578

Alfa AF: 0.531 Hom.: 2711

Bravo AF: 0.558

Asia WGS AF: 0.671 AC: 2333 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	5.4
Dann	Benign	0.67

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: rs11074553; hg19: chr16-23211319;