2-227623803-T-G

Variant names:

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

Variant summary

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

The ENST00000264387.8(SLC19A4P):​n.277+4636A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 151,908 control chromosomes in the GnomAD database, including 8,308 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 0.32 (8308 hom., 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.44 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC19A4P	NR_172911.1	n.425+4636A>C		intron_variant	Intron 2 of 3
SLC19A4P	NR_172912.1	n.425+4636A>C		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>C		intron_variant	Intron 2 of 2	1
SLC19A4P	ENST00000409066.1	n.425+4636A>C		intron_variant	Intron 2 of 3	2
SLC19A4P	ENST00000828057.1	n.375-3882A>C		intron_variant	Intron 2 of 2
SLC19A4P	ENST00000828058.1	n.143-3882A>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.318 AC: 48325 AN: 151790 Hom.: 8298 Cov.: 32

Gnomad AFR AF: 0.445

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.403

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.318 AC: 48378 AN: 151908 Hom.: 8308 Cov.: 32 AF XY: 0.317 AC XY: 23504 AN XY: 74256

African (AFR) AF: 0.445 AC: 18410 AN: 41364

American (AMR) AF: 0.325 AC: 4958 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.362 AC: 1254 AN: 3466

East Asian (EAS) AF: 0.219 AC: 1129 AN: 5164

South Asian (SAS) AF: 0.402 AC: 1939 AN: 4818

European-Finnish (FIN) AF: 0.153 AC: 1616 AN: 10546

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.265 AC: 17992 AN: 67978

Other (OTH) AF: 0.327 AC: 690 AN: 2112

Alfa AF: 0.288 Hom.: 1301

Bravo AF: 0.336

Asia WGS AF: 0.318 AC: 1105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.9
DANN	Benign	0.67
PhyloP100		-0.39
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: rs6436716; hg19: chr2-228488519;