18-45746254-C-T

Position:

• chr18-45746254-C-T

Variant summary

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

The NM_015865.7(SLC14A1):​c.947-2122C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 152,138 control chromosomes in the GnomAD database, including 2,321 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 0.15 (2321 hom., cov: 33)
• Consequence: SLC14A1 NM_015865.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.454

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=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.403 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC14A1	NM_015865.7	c.947-2122C>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.947-2122C>T		intron_variant		1	NM_015865.7	ENSP00000318546.4

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22170 AN: 152018 Hom.: 2312 Cov.: 33

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.0308

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.0845

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0664

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.146 AC: 22212 AN: 152138 Hom.: 2321 Cov.: 33 AF XY: 0.153 AC XY: 11374 AN XY: 74378

Gnomad4 AFR AF: 0.209

Gnomad4 AMR AF: 0.251

Gnomad4 ASJ AF: 0.0845

Gnomad4 EAS AF: 0.418

Gnomad4 SAS AF: 0.256

Gnomad4 FIN AF: 0.114

Gnomad4 NFE AF: 0.0664

Gnomad4 OTH AF: 0.122

Alfa AF: 0.0982 Hom.: 503

Bravo AF: 0.158

Asia WGS AF: 0.317 AC: 1099 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	2.5
DANN	Benign	0.77

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs900971; hg19: chr18-43326219;