chr2-227623803-T-A

Variant names:

• chr2-227623803-T-A
• rs6436716
• ENST00000264387.8:n.277+4636A>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000264387.8(SLC19A4P):​n.277+4636A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: SLC19A4P ENST00000264387.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.385
• Publications: 0 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC19A4P	NR_172911.1	n.425+4636A>T		intron_variant	Intron 2 of 3
SLC19A4P	NR_172912.1	n.425+4636A>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC19A4P	ENST00000264387.8	n.277+4636A>T		intron_variant	Intron 2 of 2	1
SLC19A4P	ENST00000409066.1	n.425+4636A>T		intron_variant	Intron 2 of 3	2
SLC19A4P	ENST00000828057.1	n.375-3882A>T		intron_variant	Intron 2 of 2
SLC19A4P	ENST00000828058.1	n.143-3882A>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.8
DANN	Benign	0.67
PhyloP100		-0.39

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: rs6436716; hg19: chr2-228488519;