17-15981247-C-T

Position:

• chr17-15981247-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.202-103G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.492 in 726,328 control chromosomes in the GnomAD database, including 91,953 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 0.48 (17830 hom., cov: 32)
  • Exomes 𝑓: 0.50 (74123 hom.)
• Consequence: ZSWIM7 NM_001042697.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69

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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.529 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZSWIM7	NM_001042697.2	c.202-103G>A		intron_variant		ENST00000399277.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZSWIM7	ENST00000399277.6	c.202-103G>A		intron_variant		1	NM_001042697.2	P1

Frequencies

GnomAD3 genomes AF: 0.476 AC: 72256 AN: 151870 Hom.: 17818 Cov.: 32

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.522

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.639

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.563

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.534

Gnomad OTH AF: 0.483

GnomAD4 exome AF: 0.496 AC: 284987 AN: 574340 Hom.: 74123 AF XY: 0.494 AC XY: 148823 AN XY: 301406

Gnomad4 AFR exome AF: 0.407

Gnomad4 AMR exome AF: 0.419

Gnomad4 ASJ exome AF: 0.636

Gnomad4 EAS exome AF: 0.136

Gnomad4 SAS exome AF: 0.405

Gnomad4 FIN exome AF: 0.562

Gnomad4 NFE exome AF: 0.533

Gnomad4 OTH exome AF: 0.502

GnomAD4 genome AF: 0.476 AC: 72316 AN: 151988 Hom.: 17830 Cov.: 32 AF XY: 0.474 AC XY: 35228 AN XY: 74320

Gnomad4 AFR AF: 0.397

Gnomad4 AMR AF: 0.465

Gnomad4 ASJ AF: 0.639

Gnomad4 EAS AF: 0.150

Gnomad4 SAS AF: 0.386

Gnomad4 FIN AF: 0.563

Gnomad4 NFE AF: 0.534

Gnomad4 OTH AF: 0.486

Alfa AF: 0.528 Hom.: 31017

Bravo AF: 0.464

Asia WGS AF: 0.322 AC: 1118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.66
DANN	Benign	0.65

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: rs10491104; hg19: chr17-15884561; COSMIC: COSV67886946; COSMIC: COSV67886946;