chr18-45745479-T-C

Position:

• chr18-45745479-T-C

Variant summary

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

The NM_015865.7(SLC14A1):​c.947-2897T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.922 in 152,160 control chromosomes in the GnomAD database, including 64,731 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 0.92 (64731 hom., cov: 30)
• Consequence: SLC14A1 NM_015865.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.485

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC14A1	NM_015865.7	c.947-2897T>C		intron_variant		ENST00000321925.9
LOC105372093	XR_935423.3	n.697+1647A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC14A1	ENST00000321925.9	c.947-2897T>C		intron_variant		1	NM_015865.7	P1

Frequencies

GnomAD3 genomes AF: 0.922 AC: 140211 AN: 152042 Hom.: 64683 Cov.: 30

Gnomad AFR AF: 0.909

Gnomad AMI AF: 0.976

Gnomad AMR AF: 0.943

Gnomad ASJ AF: 0.905

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.980

Gnomad FIN AF: 0.923

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.915

Gnomad OTH AF: 0.921

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

GnomAD4 genome AF: 0.922 AC: 140317 AN: 152160 Hom.: 64731 Cov.: 30 AF XY: 0.925 AC XY: 68809 AN XY: 74386

Gnomad4 AFR AF: 0.909

Gnomad4 AMR AF: 0.943

Gnomad4 ASJ AF: 0.905

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.980

Gnomad4 FIN AF: 0.923

Gnomad4 NFE AF: 0.915

Gnomad4 OTH AF: 0.921

Alfa AF: 0.919 Hom.: 83118

Bravo AF: 0.921

Asia WGS AF: 0.978 AC: 3402 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.46
DANN	Benign	0.53

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: rs566309; hg19: chr18-43325444;