18-45749233-A-G

Position:

• chr18-45749233-A-G

Variant summary

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

The NM_015865.7(SLC14A1):​c.997-545A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.613 in 151,914 control chromosomes in the GnomAD database, including 29,250 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 0.61 (29250 hom., cov: 31)
• Consequence: SLC14A1 NM_015865.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.580

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]

LOC105372093 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.907 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC14A1	NM_015865.7	c.997-545A>G		intron_variant		ENST00000321925.9	NP_056949.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC14A1	ENST00000321925.9	c.997-545A>G		intron_variant		1	NM_015865.7	ENSP00000318546.4

Frequencies

GnomAD3 genomes AF: 0.613 AC: 93093 AN: 151796 Hom.: 29239 Cov.: 31

Gnomad AFR AF: 0.502

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.708

Gnomad ASJ AF: 0.606

Gnomad EAS AF: 0.929

Gnomad SAS AF: 0.690

Gnomad FIN AF: 0.670

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.624

Gnomad OTH AF: 0.620

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.613 AC: 93141 AN: 151914 Hom.: 29250 Cov.: 31 AF XY: 0.616 AC XY: 45746 AN XY: 74242

Gnomad4 AFR AF: 0.502

Gnomad4 AMR AF: 0.708

Gnomad4 ASJ AF: 0.606

Gnomad4 EAS AF: 0.929

Gnomad4 SAS AF: 0.689

Gnomad4 FIN AF: 0.670

Gnomad4 NFE AF: 0.624

Gnomad4 OTH AF: 0.616

Alfa AF: 0.614 Hom.: 16236

Bravo AF: 0.611

Asia WGS AF: 0.757 AC: 2634 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.87
DANN	Benign	0.60

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: rs16809; hg19: chr18-43329198;