chr18-45730381-C-G

Variant names:

• chr18-45730381-C-G
• rs765284140
• NM_015865.7:c.61C>G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_015865.7(SLC14A1):​c.61C>G​(p.Gln21Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: SLC14A1 NM_015865.7 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.905

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 Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.070275754).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC14A1	NM_015865.7	c.61C>G	p.Gln21Glu	missense_variant	Exon 3 of 10	ENST00000321925.9	NP_056949.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC14A1	ENST00000321925.9	c.61C>G	p.Gln21Glu	missense_variant	Exon 3 of 10	1	NM_015865.7	ENSP00000318546.4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.061
BayesDel_addAF	Benign	-0.18	T
BayesDel_noAF	Benign	-0.50
CADD	Benign	8.4
DANN	Benign	0.89
DEOGEN2	Benign	0.086	T;T;.;T;.;.;T;T
Eigen	Benign	-0.64
Eigen_PC	Benign	-0.60
FATHMM_MKL	Benign	0.20	N
LIST_S2	Benign	0.63	.;T;.;.;T;T;T;.
M_CAP	Benign	0.0099	T
MetaRNN	Benign	0.070	T;T;T;T;T;T;T;T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	1.7	L;.;.;L;.;.;L;.
PrimateAI	Benign	0.25	T
PROVEAN	Benign	-0.77	N;.;N;.;.;N;.;.
REVEL	Benign	0.041
Sift	Benign	0.55	T;.;T;.;.;T;.;.
Sift4G	Benign	0.62	T;T;T;T;T;T;T;T
Polyphen		0.0	B;.;B;B;.;B;B;.
Vest4		0.12
MutPred		0.22		Loss of MoRF binding (P = 0.0708);Loss of MoRF binding (P = 0.0708);.;Loss of MoRF binding (P = 0.0708);Loss of MoRF binding (P = 0.0708);.;Loss of MoRF binding (P = 0.0708);Loss of MoRF binding (P = 0.0708);
MVP		0.47
MPC		0.11
ClinPred		0.16	T
GERP RS		3.9
Varity_R		0.10
gMVP		0.10

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: rs765284140; hg19: chr18-43310346;