1-45045427-T-C

Variant summary

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

The NM_020883.2(ZSWIM5):c.1433-2032A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.944 in 152,276 control chromosomes in the GnomAD database, including 67,877 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 0.94 (67877 hom., cov: 32)
• Consequence: ZSWIM5 NM_020883.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.207

Genes affected

ZSWIM5 (HGNC:29299): (zinc finger SWIM-type containing 5) Predicted to enable zinc ion binding activity. Located in extracellular space. [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=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.949 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZSWIM5	NM_020883.2	c.1433-2032A>G		intron_variant		ENST00000359600.6
ZSWIM5	XM_011541861.4	c.1433-2032A>G		intron_variant
ZSWIM5	XM_047426192.1	c.1433-4889A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZSWIM5	ENST00000359600.6	c.1433-2032A>G		intron_variant		1	NM_020883.2	P1

Frequencies

GnomAD3 genomes AF: 0.944 AC: 143645 AN: 152158 Hom.: 67840 Cov.: 32

Gnomad AFR AF: 0.957

Gnomad AMI AF: 0.931

Gnomad AMR AF: 0.933

Gnomad ASJ AF: 0.976

Gnomad EAS AF: 0.883

Gnomad SAS AF: 0.959

Gnomad FIN AF: 0.933

Gnomad MID AF: 0.994

Gnomad NFE AF: 0.942

Gnomad OTH AF: 0.950

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.944 AC: 143740 AN: 152276 Hom.: 67877 Cov.: 32 AF XY: 0.944 AC XY: 70293 AN XY: 74454

Gnomad4 AFR AF: 0.956

Gnomad4 AMR AF: 0.934

Gnomad4 ASJ AF: 0.976

Gnomad4 EAS AF: 0.884

Gnomad4 SAS AF: 0.959

Gnomad4 FIN AF: 0.933

Gnomad4 NFE AF: 0.942

Gnomad4 OTH AF: 0.950

Alfa AF: 0.944 Hom.: 13530

Bravo AF: 0.941

Asia WGS AF: 0.937 AC: 3260 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	11
Dann	Benign	0.80

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: rs2036426; hg19: chr1-45511099;