rs2396468

Variant names:

• chr2-227641403-C-A
• rs2396468
• ENST00000509872.1:n.997+681G>T

Variant summary

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

The ENST00000641887.1(SLC19A4P):​n.143+820G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.83 in 152,198 control chromosomes in the GnomAD database, including 52,560 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 0.83 (52560 hom., cov: 34)
• Consequence: SLC19A4P ENST00000641887.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95
• Publications: 1 publications found

Genes affected

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]

SLC19A4P (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.863 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000641887.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC19A4P	ENST00000509872.1	TSL:6	n.997+681G>T		intron	N/A
	SLC19A4P	ENST00000641887.1		n.143+820G>T		intron	N/A
	ENSG00000307693	ENST00000827917.1		n.148-7674C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.830 AC: 126255 AN: 152080 Hom.: 52506 Cov.: 34

Gnomad AFR AF: 0.787

Gnomad AMI AF: 0.887

Gnomad AMR AF: 0.814

Gnomad ASJ AF: 0.728

Gnomad EAS AF: 0.705

Gnomad SAS AF: 0.867

Gnomad FIN AF: 0.853

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.869

Gnomad OTH AF: 0.819

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

GnomAD4 genome AF: 0.830 AC: 126368 AN: 152198 Hom.: 52560 Cov.: 34 AF XY: 0.828 AC XY: 61606 AN XY: 74422

African (AFR) AF: 0.787 AC: 32648 AN: 41510

American (AMR) AF: 0.815 AC: 12451 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.728 AC: 2525 AN: 3470

East Asian (EAS) AF: 0.705 AC: 3645 AN: 5170

South Asian (SAS) AF: 0.868 AC: 4194 AN: 4834

European-Finnish (FIN) AF: 0.853 AC: 9033 AN: 10586

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.869 AC: 59118 AN: 68026

Other (OTH) AF: 0.821 AC: 1733 AN: 2112

Alfa AF: 0.850 Hom.: 75962

Bravo AF: 0.821

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.11
DANN	Benign	0.59
PhyloP100		-2.0

Splicing

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: rs2396468;

hg19: chr2-228506119;