chr18-45729946-C-T

Position:

• chr18-45729946-C-T

Variant summary

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

The ENST00000586142(SLC14A1):​c.-375C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.26 in 175,308 control chromosomes in the GnomAD database, including 7,367 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 0.25 (6220 hom., cov: 33)
  • Exomes 𝑓: 0.29 (1147 hom.)
• Consequence: SLC14A1 ENST00000586142 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539

Genes affected

SLC14A1 (HGNC:10918): (solute carrier family 14 member 1 (Kidd blood group)) The protein encoded by this gene is a membrane transporter that mediates urea transport in erythrocytes. This gene forms the basis for the Kidd blood group system. [provided by RefSeq, Mar 2009]

ENSG00000288545 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.357 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC14A1	NM_015865.7	c.-21-354C>T		intron_variant		ENST00000321925.9	NP_056949.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC14A1	ENST00000321925.9	c.-21-354C>T		intron_variant		1	NM_015865.7	ENSP00000318546.4

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38701 AN: 151996 Hom.: 6218 Cov.: 33

Gnomad AFR AF: 0.0755

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.0748

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.379

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.279

GnomAD4 exome AF: 0.294 AC: 6830 AN: 23194 Hom.: 1147 Cov.: 0 AF XY: 0.296 AC XY: 3498 AN XY: 11822

Gnomad4 AFR exome AF: 0.0673

Gnomad4 AMR exome AF: 0.217

Gnomad4 ASJ exome AF: 0.329

Gnomad4 EAS exome AF: 0.0615

Gnomad4 SAS exome AF: 0.303

Gnomad4 FIN exome AF: 0.300

Gnomad4 NFE exome AF: 0.346

Gnomad4 OTH exome AF: 0.285

GnomAD4 genome AF: 0.254 AC: 38703 AN: 152114 Hom.: 6220 Cov.: 33 AF XY: 0.253 AC XY: 18839 AN XY: 74354

Gnomad4 AFR AF: 0.0754

Gnomad4 AMR AF: 0.230

Gnomad4 ASJ AF: 0.345

Gnomad4 EAS AF: 0.0750

Gnomad4 SAS AF: 0.292

Gnomad4 FIN AF: 0.312

Gnomad4 NFE AF: 0.361

Gnomad4 OTH AF: 0.282

Alfa AF: 0.332 Hom.: 11948

Bravo AF: 0.237

Asia WGS AF: 0.201 AC: 696 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.38
DANN	Benign	0.63

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs17674580; hg19: chr18-43309911;