rs11889798

Variant names:

• chr2-227616703-C-T
• rs11889798
• ENST00000264387.8:n.278-5047G>A

Variant summary

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

The ENST00000264387.8(SLC19A4P):​n.278-5047G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 151,724 control chromosomes in the GnomAD database, including 1,615 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 0.13 (1615 hom., cov: 31)
• Consequence: SLC19A4P ENST00000264387.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.298
• Publications: 5 publications found

Genes affected

SLC19A4P (HGNC:):

SLC19A4P (HGNC:25344): (chromosome 2 open reading frame 83) Predicted to enable vitamin transmembrane transporter activity. Predicted to be involved in vitamin transmembrane transport. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.306 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000264387.8. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC19A4P	NR_172911.1		n.426-3669G>A		intron	N/A
	SLC19A4P	NR_172912.1		n.426-5047G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC19A4P	ENST00000264387.8	TSL:1	n.278-5047G>A		intron	N/A
	SLC19A4P	ENST00000409066.1	TSL:2	n.426-3669G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19093 AN: 151604 Hom.: 1606 Cov.: 31

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.0670

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.0663

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.0636

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.126 AC: 19113 AN: 151724 Hom.: 1615 Cov.: 31 AF XY: 0.126 AC XY: 9360 AN XY: 74134

African (AFR) AF: 0.218 AC: 9000 AN: 41326

American (AMR) AF: 0.141 AC: 2157 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 356 AN: 3466

East Asian (EAS) AF: 0.319 AC: 1636 AN: 5126

South Asian (SAS) AF: 0.125 AC: 598 AN: 4772

European-Finnish (FIN) AF: 0.0663 AC: 699 AN: 10540

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.0635 AC: 4318 AN: 67948

Other (OTH) AF: 0.115 AC: 241 AN: 2098

Alfa AF: 0.0893 Hom.: 3317

Bravo AF: 0.138

Asia WGS AF: 0.207 AC: 717 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.1
DANN	Benign	0.30
PhyloP100		0.30
PromoterAI		0.030	Neutral
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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11889798;

hg19: chr2-228481419;