rs1961669

Positions:

• chr17-19570207-A-G

Variant summary

Our verdict is Benign. Variant got -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

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC47A1	NM_018242.3	c.1310-1271A>G		intron_variant		ENST00000270570.8
LOC105371578	XR_934310.4	n.634+638T>C		intron_variant, non_coding_transcript_variant
LOC105371578	XR_001752814.3	n.634+638T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC47A1	ENST00000270570.8	c.1310-1271A>G		intron_variant		1	NM_018242.3	P1
	ENST00000574267.1	n.208+638T>C		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.189

Gnomad4 ASJ AF: 0.107

Gnomad4 EAS AF: 0.294

Gnomad4 SAS AF: 0.250

Gnomad4 FIN AF: 0.211

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.153

Alfa AF: 0.172 Hom.: 1309

Bravo AF: 0.159

Asia WGS AF: 0.230 AC: 800 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.17
DANN	Benign	0.50

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

Publications

LitVar

Other links and lift over

dbSNP: rs1961669; hg19: chr17-19473520;