rs2245639

Positions:

• chr17-19590865-C-A
• chr17-19590865-C-G
• chr17-19590865-C-T

Variant summary

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

The ENST00000420951.1(ENSG00000290454):​n.273-3345C>A 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 0.555 in 152,026 control chromosomes in the GnomAD database, including 24,191 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 0.56 (24191 hom., cov: 32)
  • Exomes 𝑓: 0.17 (0 hom.)
• Consequence: ENST00000420951.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.140

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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.931 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.273-3345C>A		intron_variant, non_coding_transcript_variant		5
SLC47A1P1	ENST00000449666.3	n.652+77C>A		intron_variant, non_coding_transcript_variant
	ENST00000574267.1	n.26+7032G>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.555 AC: 84342 AN: 151900 Hom.: 24149 Cov.: 32

Gnomad AFR AF: 0.488

Gnomad AMI AF: 0.603

Gnomad AMR AF: 0.666

Gnomad ASJ AF: 0.482

Gnomad EAS AF: 0.953

Gnomad SAS AF: 0.681

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.545

Gnomad OTH AF: 0.555

GnomAD4 exome AF: 0.167 AC: 1 AN: 6 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 FIN exome AF: 0.250

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.555 AC: 84435 AN: 152020 Hom.: 24191 Cov.: 32 AF XY: 0.562 AC XY: 41735 AN XY: 74306

Gnomad4 AFR AF: 0.488

Gnomad4 AMR AF: 0.666

Gnomad4 ASJ AF: 0.482

Gnomad4 EAS AF: 0.953

Gnomad4 SAS AF: 0.681

Gnomad4 FIN AF: 0.489

Gnomad4 NFE AF: 0.545

Gnomad4 OTH AF: 0.560

Alfa AF: 0.540 Hom.: 23402

Bravo AF: 0.563

Asia WGS AF: 0.805 AC: 2796 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.6
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2245639; hg19: chr17-19494178;