rs2120273

Positions:

• chr17-19582422-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+2087T>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 0.194 in 151,696 control chromosomes in the GnomAD database, including 2,675 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 0.19 (2672 hom., cov: 32)
  • Exomes 𝑓: 0.23 (3 hom.)
• Consequence: ENST00000420951.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.252

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.225 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000420951.1	n.272+2087T>C		intron_variant, non_coding_transcript_variant		5
SLC47A1P1	ENST00000449666.3	n.347+2087T>C		intron_variant, non_coding_transcript_variant
	ENST00000574267.1	n.27-11396A>G		intron_variant, non_coding_transcript_variant		5
	ENST00000454535.5	n.129+867T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29372 AN: 151482 Hom.: 2667 Cov.: 32

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.197

GnomAD4 exome AF: 0.228 AC: 21 AN: 92 Hom.: 3 AF XY: 0.171 AC XY: 12 AN XY: 70

Gnomad4 AFR exome AF: 0.00

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.333

Gnomad4 NFE exome AF: 0.194

Gnomad4 OTH exome AF: 0.400

GnomAD4 genome AF: 0.194 AC: 29401 AN: 151604 Hom.: 2672 Cov.: 32 AF XY: 0.191 AC XY: 14186 AN XY: 74120

Gnomad4 AFR AF: 0.181

Gnomad4 AMR AF: 0.231

Gnomad4 ASJ AF: 0.122

Gnomad4 EAS AF: 0.234

Gnomad4 SAS AF: 0.183

Gnomad4 FIN AF: 0.169

Gnomad4 NFE AF: 0.200

Gnomad4 OTH AF: 0.197

Alfa AF: 0.197 Hom.: 330

Asia WGS AF: 0.210 AC: 734 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.1
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2120273; hg19: chr17-19485735;