17-15980913-A-G

Position:

• chr17-15980913-A-G

Variant summary

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

The NM_001042697.2(ZSWIM7):​c.306+127T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.573 in 617,924 control chromosomes in the GnomAD database, including 104,911 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 0.60 (27968 hom., cov: 31)
  • Exomes 𝑓: 0.56 (76943 hom.)
• Consequence: ZSWIM7 NM_001042697.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.196

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.69 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZSWIM7	NM_001042697.2	c.306+127T>C		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+127T>C		intron_variant		1	NM_001042697.2	ENSP00000382218	P1

Frequencies

GnomAD3 genomes AF: 0.600 AC: 91123 AN: 151928 Hom.: 27915 Cov.: 31

Gnomad AFR AF: 0.697

Gnomad AMI AF: 0.538

Gnomad AMR AF: 0.540

Gnomad ASJ AF: 0.682

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.530

Gnomad FIN AF: 0.608

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.580

Gnomad OTH AF: 0.589

GnomAD4 exome AF: 0.564 AC: 262870 AN: 465878 Hom.: 76943 AF XY: 0.564 AC XY: 135057 AN XY: 239330

Gnomad4 AFR exome AF: 0.706

Gnomad4 AMR exome AF: 0.496

Gnomad4 ASJ exome AF: 0.680

Gnomad4 EAS exome AF: 0.246

Gnomad4 SAS exome AF: 0.554

Gnomad4 FIN exome AF: 0.603

Gnomad4 NFE exome AF: 0.583

Gnomad4 OTH exome AF: 0.578

GnomAD4 genome AF: 0.600 AC: 91245 AN: 152046 Hom.: 27968 Cov.: 31 AF XY: 0.598 AC XY: 44443 AN XY: 74304

Gnomad4 AFR AF: 0.697

Gnomad4 AMR AF: 0.541

Gnomad4 ASJ AF: 0.682

Gnomad4 EAS AF: 0.269

Gnomad4 SAS AF: 0.531

Gnomad4 FIN AF: 0.608

Gnomad4 NFE AF: 0.580

Gnomad4 OTH AF: 0.593

Alfa AF: 0.587 Hom.: 3108

Bravo AF: 0.596

Asia WGS AF: 0.466 AC: 1617 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.1
DANN	Benign	0.60

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: rs2286796; hg19: chr17-15884227; COSMIC: COSV67886921; COSMIC: COSV67886921;