rs17775170

Variant names:

• chr2-102635468-G-A
• rs17775170
• NM_003048.6:c.289+15331G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-102635468-G-A
• chr2-102635468-G-C

Variant summary

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

The NM_003048.6(SLC9A2):​c.289+15331G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 152,142 control chromosomes in the GnomAD database, including 2,931 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).

• Frequency: Genomes: 𝑓 0.18 (2931 hom., cov: 33)
• Consequence: SLC9A2 NM_003048.6 intron
• Clinical Significance: association no assertion criteria provided O:1
• Conservation: PhyloP100: -0.437
• Publications: 8 publications found

Genes affected

SLC9A2 (HGNC:11072): (solute carrier family 9 member A2) This gene encodes a member of the sodium-hydrogen exchanger (NHE) protein family. These proteins are involved in sodium-ion transport by exchanging intracellular hydrogen ions to external sodium ions and help in the regulation of cell pH and volume. The encoded protein is localized to the apical membrane and is involved in apical absorption of sodium. [provided by RefSeq, Jun 2016]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.296 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003048.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC9A2	NM_003048.6	MANE Select	c.289+15331G>A		intron	N/A	NP_003039.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC9A2	ENST00000233969.3	TSL:1 MANE Select	c.289+15331G>A		intron	N/A	ENSP00000233969.2	Q9UBY0
	SLC9A2	ENST00000907278.1		c.289+15331G>A		intron	N/A	ENSP00000577337.1
	SLC9A2	ENST00000907277.1		c.289+15331G>A		intron	N/A	ENSP00000577336.1

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27079 AN: 152024 Hom.: 2923 Cov.: 33

Gnomad AFR AF: 0.0801

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.178 AC: 27102 AN: 152142 Hom.: 2931 Cov.: 33 AF XY: 0.179 AC XY: 13330 AN XY: 74386

African (AFR) AF: 0.0801 AC: 3325 AN: 41506

American (AMR) AF: 0.303 AC: 4636 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 438 AN: 3472

East Asian (EAS) AF: 0.229 AC: 1185 AN: 5172

South Asian (SAS) AF: 0.204 AC: 986 AN: 4826

European-Finnish (FIN) AF: 0.172 AC: 1821 AN: 10592

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.208 AC: 14111 AN: 67976

Other (OTH) AF: 0.163 AC: 345 AN: 2114

Alfa AF: 0.199 Hom.: 1750

Bravo AF: 0.185

Asia WGS AF: 0.208 AC: 724 AN: 3478

ClinVar

ClinVar submissions

Significance: association

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
-	-	-	Ascending aortic dissection (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.57
DANN	Benign	0.66
PhyloP100		-0.44
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

Other links and lift over

dbSNP: rs17775170; hg19: chr2-103251927;