1-45045427-T-C

Variant names:

• chr1-45045427-T-C
• rs2036426
• NM_020883.2:c.1433-2032A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020883.2. 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
	ZSWIM5	NM_020883.2	MANE Select	c.1433-2032A>G		intron	N/A	NP_065934.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZSWIM5	ENST00000359600.6	TSL:1 MANE Select	c.1433-2032A>G		intron	N/A	ENSP00000352614.5

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

African (AFR) AF: 0.956 AC: 39754 AN: 41564

American (AMR) AF: 0.934 AC: 14277 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.976 AC: 3390 AN: 3472

East Asian (EAS) AF: 0.884 AC: 4574 AN: 5176

South Asian (SAS) AF: 0.959 AC: 4624 AN: 4822

European-Finnish (FIN) AF: 0.933 AC: 9897 AN: 10604

Middle Eastern (MID) AF: 0.990 AC: 291 AN: 294

European-Non Finnish (NFE) AF: 0.942 AC: 64079 AN: 68028

Other (OTH) AF: 0.950 AC: 2005 AN: 2110

Alfa AF: 0.942 Hom.: 92935

Bravo AF: 0.941

Asia WGS AF: 0.937 AC: 3260 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	11
DANN	Benign	0.80
PhyloP100		-0.21
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: rs2036426; hg19: chr1-45511099;