2-227644742-C-T

Variant names:

• chr2-227644742-C-T
• rs997363
• ENST00000509872.1:n.805-2466G>A

Variant summary

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

The ENST00000509872.1(SLC19A4P):​n.805-2466G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.636 in 151,798 control chromosomes in the GnomAD database, including 31,164 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 0.64 (31164 hom., cov: 30)
• Consequence: SLC19A4P ENST00000509872.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.130
• Publications: 8 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]

ENSG00000307693 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.747 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC19A4P	ENST00000509872.1	n.805-2466G>A		intron_variant	Intron 2 of 3	6
ENSG00000307693	ENST00000827917.1	n.148-4335C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.636 AC: 96465 AN: 151680 Hom.: 31131 Cov.: 30

Gnomad AFR AF: 0.754

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.580

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.572

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.595

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.611

Gnomad OTH AF: 0.609

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

GnomAD4 genome AF: 0.636 AC: 96539 AN: 151798 Hom.: 31164 Cov.: 30 AF XY: 0.631 AC XY: 46779 AN XY: 74182

African (AFR) AF: 0.754 AC: 31209 AN: 41400

American (AMR) AF: 0.580 AC: 8836 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.487 AC: 1688 AN: 3468

East Asian (EAS) AF: 0.571 AC: 2937 AN: 5144

South Asian (SAS) AF: 0.449 AC: 2161 AN: 4810

European-Finnish (FIN) AF: 0.595 AC: 6251 AN: 10500

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.611 AC: 41516 AN: 67922

Other (OTH) AF: 0.605 AC: 1275 AN: 2106

Alfa AF: 0.609 Hom.: 32102

Bravo AF: 0.642

Asia WGS AF: 0.531 AC: 1847 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.4
DANN	Benign	0.72
PhyloP100		-0.13

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs997363; hg19: chr2-228509458;