rs10179572

Variant names:

• chr2-227639787-A-G
• rs10179572
• ENST00000509872.1:n.997+2297T>C

Variant summary

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

The ENST00000641887.1(SLC19A4P):​n.143+2436T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.381 in 151,878 control chromosomes in the GnomAD database, including 11,594 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 0.38 (11594 hom., cov: 31)
• Consequence: SLC19A4P ENST00000641887.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.537
• Publications: 4 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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.456 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+2297T>C		intron	N/A
	SLC19A4P	ENST00000641887.1		n.143+2436T>C		intron	N/A
	ENSG00000307693	ENST00000827917.1		n.148-9290A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.381 AC: 57771 AN: 151760 Hom.: 11581 Cov.: 31

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.461

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.291

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.478

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.381 AC: 57806 AN: 151878 Hom.: 11594 Cov.: 31 AF XY: 0.378 AC XY: 28088 AN XY: 74226

African (AFR) AF: 0.262 AC: 10858 AN: 41398

American (AMR) AF: 0.377 AC: 5755 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.252 AC: 874 AN: 3470

East Asian (EAS) AF: 0.291 AC: 1503 AN: 5170

South Asian (SAS) AF: 0.259 AC: 1248 AN: 4816

European-Finnish (FIN) AF: 0.478 AC: 5030 AN: 10534

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.460 AC: 31236 AN: 67926

Other (OTH) AF: 0.375 AC: 789 AN: 2106

Alfa AF: 0.404 Hom.: 8673

Bravo AF: 0.367

Asia WGS AF: 0.313 AC: 1087 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.7
DANN	Benign	0.50
PhyloP100		0.54

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: rs10179572;

hg19: chr2-228504503;