chr17-15980495-C-T

Position:

• chr17-15980495-C-T

Variant summary

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

The NM_001042697.2(ZSWIM7):​c.306+545G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.643 in 152,158 control chromosomes in the GnomAD database, including 32,938 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 0.64 (32925 hom., cov: 32)
  • Exomes 𝑓: 0.58 (13 hom.)
• Consequence: ZSWIM7 NM_001042697.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.791

Genes affected

ZSWIM7 (HGNC:26993): (zinc finger SWIM-type containing 7) Predicted to enable zinc ion binding activity. Involved in double-strand break repair via homologous recombination and protein stabilization. Part of Shu complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.838 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZSWIM7	NM_001042697.2	c.306+545G>A		intron_variant		ENST00000399277.6	NP_001036162.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZSWIM7	ENST00000399277.6	c.306+545G>A		intron_variant		1	NM_001042697.2	ENSP00000382218	P1

Frequencies

GnomAD3 genomes AF: 0.642 AC: 97617 AN: 151962 Hom.: 32862 Cov.: 32

Gnomad AFR AF: 0.845

Gnomad AMI AF: 0.538

Gnomad AMR AF: 0.555

Gnomad ASJ AF: 0.683

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.528

Gnomad FIN AF: 0.608

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.581

Gnomad OTH AF: 0.621

GnomAD4 exome AF: 0.577 AC: 45 AN: 78 Hom.: 13 AF XY: 0.548 AC XY: 23 AN XY: 42

Gnomad4 AFR exome AF: 0.500

Gnomad4 AMR exome AF: 0.500

Gnomad4 FIN exome AF: 0.250

Gnomad4 NFE exome AF: 0.609

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.643 AC: 97753 AN: 152080 Hom.: 32925 Cov.: 32 AF XY: 0.638 AC XY: 47435 AN XY: 74332

Gnomad4 AFR AF: 0.846

Gnomad4 AMR AF: 0.556

Gnomad4 ASJ AF: 0.683

Gnomad4 EAS AF: 0.268

Gnomad4 SAS AF: 0.530

Gnomad4 FIN AF: 0.608

Gnomad4 NFE AF: 0.580

Gnomad4 OTH AF: 0.624

Alfa AF: 0.614 Hom.: 6085

Bravo AF: 0.644

Asia WGS AF: 0.467 AC: 1623 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.38
DANN	Benign	0.56

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2286795; hg19: chr17-15883809; COSMIC: COSV58481791; COSMIC: COSV58481791;