18-45723869-C-T

Variant names:

• chr18-45723869-C-T
• rs1484878
• ENST00000644925.1:n.543C>T

Variant summary

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

The ENST00000644925.1(SLC14A1):​n.543C>T 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 0.783 in 152,142 control chromosomes in the GnomAD database, including 47,099 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 0.78 (47095 hom., cov: 32)
  • Exomes 𝑓: 0.83 (4 hom.)
• Consequence: SLC14A1 ENST00000644925.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.830
• Publications: 6 publications found

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

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 = 0.851 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000644925.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC14A1	ENST00000644925.1		n.543C>T		non_coding_transcript_exon	Exon 3 of 4
	ENSG00000288545	ENST00000589510.5	TSL:5	n.160+13597G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.783 AC: 119014 AN: 152012 Hom.: 47074 Cov.: 32

Gnomad AFR AF: 0.685

Gnomad AMI AF: 0.947

Gnomad AMR AF: 0.773

Gnomad ASJ AF: 0.808

Gnomad EAS AF: 0.591

Gnomad SAS AF: 0.704

Gnomad FIN AF: 0.801

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.857

Gnomad OTH AF: 0.811

GnomAD4 exome AF: 0.833 AC: 10 AN: 12 Hom.: 4 Cov.: 0 AF XY: 1.00 AC XY: 4 AN XY: 4

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) AF: 1.00 AC: 4 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.833 AC: 5 AN: 6

Other (OTH) AF: 0.500 AC: 1 AN: 2

GnomAD4 genome AF: 0.783 AC: 119089 AN: 152130 Hom.: 47095 Cov.: 32 AF XY: 0.778 AC XY: 57865 AN XY: 74366

African (AFR) AF: 0.686 AC: 28419 AN: 41456

American (AMR) AF: 0.772 AC: 11817 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.808 AC: 2804 AN: 3472

East Asian (EAS) AF: 0.592 AC: 3057 AN: 5164

South Asian (SAS) AF: 0.703 AC: 3385 AN: 4814

European-Finnish (FIN) AF: 0.801 AC: 8481 AN: 10592

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.857 AC: 58301 AN: 68012

Other (OTH) AF: 0.812 AC: 1714 AN: 2112

Alfa AF: 0.830 Hom.: 90455

Bravo AF: 0.776

Asia WGS AF: 0.659 AC: 2297 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.3
DANN	Benign	0.69
PhyloP100		-0.83
PromoterAI		-0.0015	Neutral

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1484878; hg19: chr18-43303834;