rs12605147

chr18-45730215-A-G

Variant summary

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

The ENST00000586142.5(SLC14A1):c.-106A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 1,396,834 control chromosomes in the GnomAD database, including 11,346 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 0.14 (1969 hom., cov: 33)
  • Exomes 𝑓: 0.096 (9377 hom.)
• Consequence: SLC14A1 ENST00000586142.5 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.306

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC14A1	NM_015865.7	c.-21-85A>G		intron_variant		ENST00000321925.9
LOC105372093	XR_935423.3	n.826+7251T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC14A1	ENST00000321925.9	c.-21-85A>G		intron_variant		1	NM_015865.7	P1
	ENST00000589510.5	n.160+7251T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.138 AC: 20932 AN: 152058 Hom.: 1966 Cov.: 33

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.0769

Gnomad NFE AF: 0.0679

Gnomad OTH AF: 0.113

GnomAD4 exome AF: 0.0960 AC: 119518 AN: 1244658 Hom.: 9377 Cov.: 17 AF XY: 0.0994 AC XY: 61112 AN XY: 614522

Gnomad4 AFR exome AF: 0.199

Gnomad4 AMR exome AF: 0.208

Gnomad4 ASJ exome AF: 0.0976

Gnomad4 EAS exome AF: 0.390

Gnomad4 SAS exome AF: 0.250

Gnomad4 FIN exome AF: 0.115

Gnomad4 NFE exome AF: 0.0655

Gnomad4 OTH exome AF: 0.115

GnomAD4 genome AF: 0.138 AC: 20960 AN: 152176 Hom.: 1969 Cov.: 33 AF XY: 0.145 AC XY: 10791 AN XY: 74414

Gnomad4 AFR AF: 0.197

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.100

Gnomad4 EAS AF: 0.406

Gnomad4 SAS AF: 0.268

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.0679

Gnomad4 OTH AF: 0.112

Alfa AF: 0.104 Hom.: 142

Bravo AF: 0.143

Asia WGS AF: 0.316 AC: 1095 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
Cadd	Benign	6.9
Dann	Benign	0.86

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: rs12605147; hg19: chr18-43310180;