17-19631121-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_170227.1(SLC47A1P2):n.751+360A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.47 in 150,784 control chromosomes in the GnomAD database, including 18,228 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 0.47 (18228 hom., cov: 30)
• Consequence: SLC47A1P2 NR_170227.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19

Genes affected

(HGNC:):

SLC47A1P2 (HGNC:53866): (SLC47A1 pseudogene 2)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.582 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC47A1P2	NR_170227.1	n.751+360A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000452153.4	n.330+360A>G		intron_variant, non_coding_transcript_variant		2
SLC47A1P2	ENST00000574288.2	n.419+369A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.470 AC: 70860 AN: 150668 Hom.: 18217 Cov.: 30

Gnomad AFR AF: 0.589

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.0907

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.470 AC: 70891 AN: 150784 Hom.: 18228 Cov.: 30 AF XY: 0.463 AC XY: 34154 AN XY: 73706

Gnomad4 AFR AF: 0.588

Gnomad4 AMR AF: 0.345

Gnomad4 ASJ AF: 0.529

Gnomad4 EAS AF: 0.0909

Gnomad4 SAS AF: 0.327

Gnomad4 FIN AF: 0.512

Gnomad4 NFE AF: 0.458

Gnomad4 OTH AF: 0.464

Alfa AF: 0.432 Hom.: 4726

Bravo AF: 0.466

Asia WGS AF: 0.217 AC: 757 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	1.1
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9903027; hg19: chr17-19534434;