NM_015865.7:c.663+353T>C

Variant names:

• chr18-45737001-T-C
• rs7238033
• NM_015865.7:c.663+353T>C

Variant summary

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

The NM_015865.7(SLC14A1):​c.663+353T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.61 in 151,418 control chromosomes in the GnomAD database, including 28,715 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 0.61 (28715 hom., cov: 30)
• Consequence: SLC14A1 NM_015865.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.12
• Publications: 28 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.906 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015865.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC14A1	NM_015865.7	MANE Select	c.663+353T>C		intron	N/A	NP_056949.4
	SLC14A1	NM_001128588.4		c.831+353T>C		intron	N/A	NP_001122060.3
	SLC14A1	NM_001146037.1		c.831+353T>C		intron	N/A	NP_001139509.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC14A1	ENST00000321925.9	TSL:1 MANE Select	c.663+353T>C		intron	N/A	ENSP00000318546.4
	SLC14A1	ENST00000586142.5	TSL:1	c.663+353T>C		intron	N/A	ENSP00000470476.1
	SLC14A1	ENST00000589700.5	TSL:1	c.663+353T>C		intron	N/A	ENSP00000465044.1

Frequencies

GnomAD3 genomes AF: 0.610 AC: 92268 AN: 151300 Hom.: 28688 Cov.: 30

Gnomad AFR AF: 0.648

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.686

Gnomad ASJ AF: 0.519

Gnomad EAS AF: 0.928

Gnomad SAS AF: 0.678

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.548

Gnomad NFE AF: 0.553

Gnomad OTH AF: 0.596

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

GnomAD4 genome AF: 0.610 AC: 92344 AN: 151418 Hom.: 28715 Cov.: 30 AF XY: 0.613 AC XY: 45274 AN XY: 73896

African (AFR) AF: 0.648 AC: 26714 AN: 41248

American (AMR) AF: 0.687 AC: 10444 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.519 AC: 1798 AN: 3466

East Asian (EAS) AF: 0.928 AC: 4766 AN: 5138

South Asian (SAS) AF: 0.677 AC: 3258 AN: 4810

European-Finnish (FIN) AF: 0.587 AC: 6079 AN: 10352

Middle Eastern (MID) AF: 0.559 AC: 162 AN: 290

European-Non Finnish (NFE) AF: 0.553 AC: 37514 AN: 67898

Other (OTH) AF: 0.594 AC: 1250 AN: 2104

Alfa AF: 0.574 Hom.: 83502

Bravo AF: 0.619

Asia WGS AF: 0.770 AC: 2679 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.14
DANN	Benign	0.73
PhyloP100		-2.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7238033; hg19: chr18-43316966;