chr18-45738290-A-G

Variant names:

• chr18-45738290-A-G
• rs11877720
• NM_015865.7:c.664-873A>G

Variant summary

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

The NM_015865.7(SLC14A1):​c.664-873A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.443 in 152,050 control chromosomes in the GnomAD database, including 15,341 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 0.44 (15341 hom., cov: 32)
• Consequence: SLC14A1 NM_015865.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0960

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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.505 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC14A1	NM_015865.7	c.664-873A>G		intron_variant	Intron 6 of 9	ENST00000321925.9	NP_056949.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC14A1	ENST00000321925.9	c.664-873A>G		intron_variant	Intron 6 of 9	1	NM_015865.7	ENSP00000318546.4

Frequencies

GnomAD3 genomes AF: 0.443 AC: 67358 AN: 151932 Hom.: 15339 Cov.: 32

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.520

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.459

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

GnomAD4 genome AF: 0.443 AC: 67378 AN: 152050 Hom.: 15341 Cov.: 32 AF XY: 0.441 AC XY: 32773 AN XY: 74324

Gnomad4 AFR AF: 0.341

Gnomad4 AMR AF: 0.496

Gnomad4 ASJ AF: 0.427

Gnomad4 EAS AF: 0.521

Gnomad4 SAS AF: 0.408

Gnomad4 FIN AF: 0.479

Gnomad4 NFE AF: 0.486

Gnomad4 OTH AF: 0.458

Alfa AF: 0.477 Hom.: 25549

Bravo AF: 0.442

Asia WGS AF: 0.445 AC: 1553 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.1
DANN	Benign	0.43

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: rs11877720; hg19: chr18-43318255;