rs7208480

Positions:

• chr17-15770470-C-T

Variant summary

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

The ENST00000420606.1(ZSWIM5P1):​n.957G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 763,216 control chromosomes in the GnomAD database, including 36,459 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 0.28 (6133 hom., cov: 31)
  • Exomes 𝑓: 0.31 (30326 hom.)
• Consequence: ZSWIM5P1 ENST00000420606.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66

Genes affected

ZSWIM5P1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZSWIM5P1		n.15770470C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZSWIM5P1	ENST00000420606.1	n.957G>A		non_coding_transcript_exon_variant	1/2	6

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42260 AN: 151654 Hom.: 6131 Cov.: 31

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.280

GnomAD4 exome AF: 0.309 AC: 188671 AN: 611444 Hom.: 30326 Cov.: 7 AF XY: 0.307 AC XY: 102191 AN XY: 333100

Gnomad4 AFR exome AF: 0.229

Gnomad4 AMR exome AF: 0.439

Gnomad4 ASJ exome AF: 0.338

Gnomad4 EAS exome AF: 0.402

Gnomad4 SAS exome AF: 0.278

Gnomad4 FIN exome AF: 0.327

Gnomad4 NFE exome AF: 0.290

Gnomad4 OTH exome AF: 0.299

GnomAD4 genome AF: 0.279 AC: 42292 AN: 151772 Hom.: 6133 Cov.: 31 AF XY: 0.283 AC XY: 20992 AN XY: 74186

Gnomad4 AFR AF: 0.217

Gnomad4 AMR AF: 0.348

Gnomad4 ASJ AF: 0.342

Gnomad4 EAS AF: 0.341

Gnomad4 SAS AF: 0.279

Gnomad4 FIN AF: 0.321

Gnomad4 NFE AF: 0.284

Gnomad4 OTH AF: 0.280

Alfa AF: 0.288 Hom.: 1456

Bravo AF: 0.281

Asia WGS AF: 0.306 AC: 1062 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	1.7
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7208480; hg19: chr17-15673784; COSMIC: COSV70507291;