17-15981247-C-T

Variant names:

• chr17-15981247-C-T
• rs10491104
• NM_001042697.2:c.202-103G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 30 publications found

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]

ZSWIM7 Gene-Disease associations (from GenCC):

• male infertility with azoospermia or oligozoospermia due to single gene mutation

  Inheritance: AR Classification: STRONG Submitted by: King Faisal Specialist Hospital and Research Center
• ovarian dysgenesis 10

  Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
• colorectal adenoma

  Inheritance: Unknown Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001042697.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZSWIM7	NM_001042697.2	MANE Select	c.202-103G>A		intron	N/A	NP_001036162.1
	ZSWIM7	NM_001042698.2		c.202-103G>A		intron	N/A	NP_001036163.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZSWIM7	ENST00000399277.6	TSL:1 MANE Select	c.202-103G>A		intron	N/A	ENSP00000382218.1
	ZSWIM7	ENST00000472495.5	TSL:1	c.202-103G>A		intron	N/A	ENSP00000419138.1
	ZSWIM7	ENST00000486706.6	TSL:1	n.*212-103G>A		intron	N/A	ENSP00000463327.1

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

African (AFR) AF: 0.407 AC: 5869 AN: 14418

American (AMR) AF: 0.419 AC: 9413 AN: 22460

Ashkenazi Jewish (ASJ) AF: 0.636 AC: 9550 AN: 15024

East Asian (EAS) AF: 0.136 AC: 4256 AN: 31290

South Asian (SAS) AF: 0.405 AC: 20438 AN: 50438

European-Finnish (FIN) AF: 0.562 AC: 24197 AN: 43032

Middle Eastern (MID) AF: 0.565 AC: 1960 AN: 3468

European-Non Finnish (NFE) AF: 0.533 AC: 194516 AN: 364752

Other (OTH) AF: 0.502 AC: 14788 AN: 29458

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

African (AFR) AF: 0.397 AC: 16446 AN: 41440

American (AMR) AF: 0.465 AC: 7102 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.639 AC: 2218 AN: 3470

East Asian (EAS) AF: 0.150 AC: 772 AN: 5156

South Asian (SAS) AF: 0.386 AC: 1855 AN: 4804

European-Finnish (FIN) AF: 0.563 AC: 5951 AN: 10566

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.534 AC: 36297 AN: 67966

Other (OTH) AF: 0.486 AC: 1026 AN: 2110

Alfa AF: 0.518 Hom.: 40645

Bravo AF: 0.464

Asia WGS AF: 0.322 AC: 1118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.66
DANN	Benign	0.65
PhyloP100		-1.7
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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