chr17-19570207-A-G

Variant names:

• chr17-19570207-A-G
• rs1961669
• NM_018242.3:c.1310-1271A>G

Variant summary

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

The NM_018242.3(SLC47A1):​c.1310-1271A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 152,224 control chromosomes in the GnomAD database, including 2,272 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 0.17 (2272 hom., cov: 32)
• Consequence: SLC47A1 NM_018242.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.536
• Publications: 7 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]

ENSG00000262769 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018242.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC47A1	NM_018242.3	MANE Select	c.1310-1271A>G		intron	N/A	NP_060712.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC47A1	ENST00000270570.8	TSL:1 MANE Select	c.1310-1271A>G		intron	N/A	ENSP00000270570.4
	SLC47A1	ENST00000395585.5	TSL:1	c.1310-1271A>G		intron	N/A	ENSP00000378951.1
	SLC47A1	ENST00000571335.5	TSL:1	c.724+2979A>G		intron	N/A	ENSP00000462630.1

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25240 AN: 152106 Hom.: 2265 Cov.: 32

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.294

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.0892

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.166 AC: 25274 AN: 152224 Hom.: 2272 Cov.: 32 AF XY: 0.170 AC XY: 12642 AN XY: 74412

African (AFR) AF: 0.117 AC: 4870 AN: 41558

American (AMR) AF: 0.189 AC: 2886 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.107 AC: 371 AN: 3472

East Asian (EAS) AF: 0.294 AC: 1521 AN: 5172

South Asian (SAS) AF: 0.250 AC: 1208 AN: 4826

European-Finnish (FIN) AF: 0.211 AC: 2233 AN: 10586

Middle Eastern (MID) AF: 0.0959 AC: 28 AN: 292

European-Non Finnish (NFE) AF: 0.172 AC: 11697 AN: 68012

Other (OTH) AF: 0.153 AC: 323 AN: 2116

Alfa AF: 0.171 Hom.: 4595

Bravo AF: 0.159

Asia WGS AF: 0.230 AC: 800 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.17
DANN	Benign	0.50
PhyloP100		-0.54
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: rs1961669; hg19: chr17-19473520;