rs977516376

Variant names:

• chr18-45624672-A-C
• rs977516376
• NM_007163.4:c.8A>C

Your query was ambiguous. Multiple possible variants found:

• chr18-45624672-A-C
• chr18-45624672-A-G
• chr18-45624672-A-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_007163.4(SLC14A2):​c.8A>C​(p.Asp3Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: SLC14A2 NM_007163.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.08

Genes affected

SLC14A2 (HGNC:10919): (solute carrier family 14 member 2) The protein encoded by this gene belongs to the urea transporter family. In mammalian cells, urea is the chief end product of nitrogen catabolism, and plays an important role in the urinary concentration mechanism. This protein is expressed in the inner medulla of the kidney, and mediates rapid transepithelial urea transport across the inner medullary collecting duct. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Sep 2011]

LOC105372093 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.090515375).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC14A2	NM_007163.4	c.8A>C	p.Asp3Ala	missense_variant	Exon 2 of 20	ENST00000255226.11	NP_009094.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC14A2	ENST00000255226.11	c.8A>C	p.Asp3Ala	missense_variant	Exon 2 of 20	1	NM_007163.4	ENSP00000255226.5
SLC14A2	ENST00000586448.5	c.8A>C	p.Asp3Ala	missense_variant	Exon 3 of 21	2		ENSP00000465953.1
SLC14A2	ENST00000323329.3	n.8A>C		non_coding_transcript_exon_variant	Exon 2 of 11	2		ENSP00000320689.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.12
BayesDel_addAF	Benign	-0.11	T
BayesDel_noAF	Benign	-0.40
CADD	Benign	22
DANN	Uncertain	0.99
DEOGEN2	Benign	0.15	T;T
Eigen	Benign	-0.37
Eigen_PC	Benign	-0.36
FATHMM_MKL	Benign	0.16	N
M_CAP	Benign	0.017	T
MetaRNN	Benign	0.091	T;T
MetaSVM	Benign	-0.88	T
MutationAssessor	Uncertain	2.1	M;M
PrimateAI	Benign	0.40	T
PROVEAN	Benign	-0.27	.;N
REVEL	Benign	0.15
Sift	Uncertain	0.0070	.;D
Sift4G	Uncertain	0.011	D;D
Polyphen		0.079	B;B
Vest4		0.37
MutPred		0.13		Gain of glycosylation at S2 (P = 0.0906);Gain of glycosylation at S2 (P = 0.0906);
MVP		0.38
MPC		0.36
ClinPred		0.74	D
GERP RS		4.9
Varity_R		0.10
gMVP		0.74

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs977516376; hg19: chr18-43204637;