rs1054986

Variant names:

• chr18-45438299-T-C
• rs1054986
• ENST00000592286.1:n.415A>G

Your query was ambiguous. Multiple possible variants found:

• chr18-45438299-T-C
• chr18-45438299-T-G

Variant summary

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

The ENST00000592286.1(SLC14A2-AS1):​n.415A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.355 in 152,070 control chromosomes in the GnomAD database, including 11,581 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 0.35 (11581 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: SLC14A2-AS1 ENST00000592286.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.267
• Publications: 2 publications found

Genes affected

SLC14A2-AS1 (HGNC:51125): (SLC14A2 antisense RNA 1)

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.466 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC14A2	NM_001242692.2	c.-124-44934T>C		intron_variant	Intron 1 of 20		NP_001229621.1
SLC14A2	NM_001371319.1	c.-124-44934T>C		intron_variant	Intron 4 of 23		NP_001358248.1
SLC14A2	XM_024451270.2	c.-124-44934T>C		intron_variant	Intron 2 of 21		XP_024307038.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC14A2-AS1	ENST00000592286.1	n.415A>G		non_coding_transcript_exon_variant	Exon 2 of 2	4
SLC14A2-AS1	ENST00000592899.2	n.519A>G		non_coding_transcript_exon_variant	Exon 5 of 5	3
SLC14A2-AS1	ENST00000716840.1	n.287A>G		non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.355 AC: 53982 AN: 151952 Hom.: 11582 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.603

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.373

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.355 AC: 53971 AN: 152070 Hom.: 11581 Cov.: 32 AF XY: 0.355 AC XY: 26365 AN XY: 74326

African (AFR) AF: 0.104 AC: 4303 AN: 41532

American (AMR) AF: 0.409 AC: 6245 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.525 AC: 1821 AN: 3468

East Asian (EAS) AF: 0.313 AC: 1611 AN: 5154

South Asian (SAS) AF: 0.342 AC: 1644 AN: 4802

European-Finnish (FIN) AF: 0.467 AC: 4930 AN: 10554

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.470 AC: 31961 AN: 67972

Other (OTH) AF: 0.370 AC: 780 AN: 2110

Alfa AF: 0.402 Hom.: 8848

Bravo AF: 0.339

Asia WGS AF: 0.306 AC: 1063 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.65
DANN	Benign	0.73
PhyloP100		-0.27
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: rs1054986; hg19: chr18-43018264;