rs2453594

Positions:

• chr17-19581638-T-C

Variant summary

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

The ENST00000420951.1(ENSG00000290454):​n.272+1303T>C 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 0.221 in 152,126 control chromosomes in the GnomAD database, including 3,897 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 0.22 (3895 hom., cov: 31)
  • Exomes 𝑓: 0.21 (2 hom.)
• Consequence: ENST00000420951.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.232

Genes affected

(HGNC:):

SLC47A1P1 (HGNC:51849): (SLC47A1 pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.294 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000420951.1	n.272+1303T>C		intron_variant, non_coding_transcript_variant		5
SLC47A1P1	ENST00000449666.3	n.347+1303T>C		intron_variant, non_coding_transcript_variant
	ENST00000574267.1	n.27-10612A>G		intron_variant, non_coding_transcript_variant		5
	ENST00000454535.5	n.129+83T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.221 AC: 33517 AN: 151940 Hom.: 3865 Cov.: 31

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.0980

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.282

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.217

GnomAD4 exome AF: 0.206 AC: 14 AN: 68 Hom.: 2 AF XY: 0.273 AC XY: 12 AN XY: 44

Gnomad4 AFR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.286

Gnomad4 OTH exome AF: 0.200

GnomAD4 genome AF: 0.221 AC: 33593 AN: 152058 Hom.: 3895 Cov.: 31 AF XY: 0.219 AC XY: 16270 AN XY: 74338

Gnomad4 AFR AF: 0.298

Gnomad4 AMR AF: 0.236

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.282

Gnomad4 SAS AF: 0.205

Gnomad4 FIN AF: 0.149

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.217

Alfa AF: 0.191 Hom.: 4829

Bravo AF: 0.233

Asia WGS AF: 0.240 AC: 838 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2453594; hg19: chr17-19484951;