rs7208480

Variant names:

• chr17-15770470-C-T
• rs7208480
• ENST00000420606.1:n.957G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

Genes affected

ZSWIM5P1 (HGNC:43768): (zinc finger SWIM-type containing 5 pseudogene 1)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ZSWIM5P1		n.15770470C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZSWIM5P1	ENST00000420606.1	n.957G>A		non_coding_transcript_exon_variant	Exon 1 of 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

African (AFR) AF: 0.229 AC: 3829 AN: 16732

American (AMR) AF: 0.439 AC: 18387 AN: 41840

Ashkenazi Jewish (ASJ) AF: 0.338 AC: 6416 AN: 18966

East Asian (EAS) AF: 0.402 AC: 12776 AN: 31784

South Asian (SAS) AF: 0.278 AC: 19224 AN: 69178

European-Finnish (FIN) AF: 0.327 AC: 15865 AN: 48582

Middle Eastern (MID) AF: 0.392 AC: 1542 AN: 3934

European-Non Finnish (NFE) AF: 0.290 AC: 101493 AN: 349844

Other (OTH) AF: 0.299 AC: 9139 AN: 30584

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

African (AFR) AF: 0.217 AC: 8956 AN: 41242

American (AMR) AF: 0.348 AC: 5313 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.342 AC: 1186 AN: 3472

East Asian (EAS) AF: 0.341 AC: 1757 AN: 5150

South Asian (SAS) AF: 0.279 AC: 1342 AN: 4806

European-Finnish (FIN) AF: 0.321 AC: 3393 AN: 10572

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.284 AC: 19296 AN: 67948

Other (OTH) AF: 0.280 AC: 591 AN: 2114

Alfa AF: 0.287 Hom.: 2533

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
PhyloP100		-1.7

Splicing

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

Other links and lift over

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