chr18-45717171-G-C

Variant names:

• chr18-45717171-G-C
• rs16978462
• ENST00000589510.5:n.160+20295C>G

Variant summary

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

The ENST00000589510.5(ENSG00000288545):​n.160+20295C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 127,392 control chromosomes in the GnomAD database, including 3,176 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 0.21 (3176 hom., cov: 26)
• Consequence: ENSG00000288545 ENST00000589510.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.416
• Publications: 4 publications found

Genes affected

ENSG00000288545 (HGNC:):

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]

ACMG classification

Our verdict: Benign. The variant received -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 = 0.587 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372092	XR_001753558.2	n.3818+205G>C		intron_variant	Intron 1 of 2
LOC105372092	XR_001753559.2	n.3818+205G>C		intron_variant	Intron 1 of 2
LOC105372092	XR_935422.3	n.3818+205G>C		intron_variant	Intron 1 of 3
LOC105372093	XR_935423.3	n.826+20295C>G		intron_variant	Intron 6 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288545	ENST00000589510.5	n.160+20295C>G		intron_variant	Intron 2 of 3	5
SLC14A1	ENST00000644925.1	n.194-4826G>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.207 AC: 26351 AN: 127358 Hom.: 3170 Cov.: 26

Gnomad AFR AF: 0.0840

Gnomad AMI AF: 0.0814

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.605

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.201

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.207 AC: 26362 AN: 127392 Hom.: 3176 Cov.: 26 AF XY: 0.210 AC XY: 12899 AN XY: 61436

African (AFR) AF: 0.0841 AC: 2818 AN: 33498

American (AMR) AF: 0.282 AC: 3599 AN: 12776

Ashkenazi Jewish (ASJ) AF: 0.206 AC: 618 AN: 3006

East Asian (EAS) AF: 0.606 AC: 2953 AN: 4876

South Asian (SAS) AF: 0.248 AC: 980 AN: 3944

European-Finnish (FIN) AF: 0.224 AC: 1578 AN: 7056

Middle Eastern (MID) AF: 0.191 AC: 39 AN: 204

European-Non Finnish (NFE) AF: 0.224 AC: 13336 AN: 59438

Other (OTH) AF: 0.213 AC: 372 AN: 1746

Alfa AF: 0.0924 Hom.: 147

Bravo AF: 0.181

Asia WGS AF: 0.321 AC: 1114 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.54
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs16978462; hg19: chr18-43297136;