rs72466470

Variant names:

• chr17-19533822-G-A
• rs72466470
• ENST00000571335.5:c.-311+251G>A

Your query was ambiguous. Multiple possible variants found:

• chr17-19533822-G-A
• chr17-19533822-G-T

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The ENST00000571335.5(SLC47A1):​c.-311+251G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000284 in 1,148,162 control chromosomes in the GnomAD database, including 3 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 0.000049 (0 hom., cov: 31)
  • Exomes 𝑓: 0.00032 (3 hom.)
• Consequence: SLC47A1 ENST00000571335.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.50
• Publications: 2 publications found

Genes affected

SLC47A1 (HGNC:25588): (solute carrier family 47 member 1) This gene is located within the Smith-Magenis syndrome region on chromosome 17. It encodes a protein of unknown function. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.47).
• BS2: High Homozygotes in GnomAdExome4 at 3 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000571335.5. 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
	SLC47A1	NM_018242.3	MANE Select	c.-118G>A		upstream_gene	N/A	NP_060712.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC47A1	ENST00000571335.5	TSL:1	c.-311+251G>A		intron	N/A	ENSP00000462630.1	J3KSS8
	SLC47A1	ENST00000901046.1		c.-118G>A		5_prime_UTR	Exon 1 of 15	ENSP00000571105.1
	SLC47A1	ENST00000584348.5	TSL:3	n.98-8571G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0000489 AC: 7 AN: 143106 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00139

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.000317 AC: 319 AN: 1004940 Hom.: 3 Cov.: 17 AF XY: 0.000265 AC XY: 126 AN XY: 475420

African (AFR) AF: 0.00 AC: 0 AN: 21082

American (AMR) AF: 0.00 AC: 0 AN: 7182

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 12800

East Asian (EAS) AF: 0.0129 AC: 317 AN: 24532

South Asian (SAS) AF: 0.00 AC: 0 AN: 19568

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 19508

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2678

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 857760

Other (OTH) AF: 0.0000502 AC: 2 AN: 39830

GnomAD4 genome AF: 0.0000489 AC: 7 AN: 143222 Hom.: 0 Cov.: 31 AF XY: 0.0000428 AC XY: 3 AN XY: 70104

African (AFR) AF: 0.00 AC: 0 AN: 39690

American (AMR) AF: 0.00 AC: 0 AN: 14232

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3320

East Asian (EAS) AF: 0.00140 AC: 7 AN: 5006

South Asian (SAS) AF: 0.00 AC: 0 AN: 4720

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 9988

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 276

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 63208

Other (OTH) AF: 0.00 AC: 0 AN: 1986

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.0000227

Asia WGS AF: 0.000578 AC: 2 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
CADD	Benign	18
DANN	Uncertain	0.98
PhyloP100		1.5
PromoterAI		-0.50	Neutral

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: rs72466470;

hg19: chr17-19437135;