chr1-45172814-T-C

Variant names:

• chr1-45172814-T-C
• rs1226749
• NM_020883.2:c.595+32942A>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.595+32942A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 152,160 control chromosomes in the GnomAD database, including 2,665 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 0.16 (2665 hom., cov: 32)
• Consequence: ZSWIM5 NM_020883.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0960
• Publications: 3 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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZSWIM5	NM_020883.2	c.595+32942A>G		intron_variant	Intron 1 of 13	ENST00000359600.6	NP_065934.1
ZSWIM5	XM_047426192.1	c.595+32942A>G		intron_variant	Intron 1 of 12		XP_047282148.1
ZSWIM5	XM_011541861.4	c.595+32942A>G		intron_variant	Intron 1 of 10		XP_011540163.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZSWIM5	ENST00000359600.6	c.595+32942A>G		intron_variant	Intron 1 of 13	1	NM_020883.2	ENSP00000352614.5
ZSWIM5	ENST00000464588.1	n.228-84577A>G		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24350 AN: 152042 Hom.: 2665 Cov.: 32

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.0834

Gnomad ASJ AF: 0.0700

Gnomad EAS AF: 0.000768

Gnomad SAS AF: 0.0757

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.160 AC: 24355 AN: 152160 Hom.: 2665 Cov.: 32 AF XY: 0.156 AC XY: 11598 AN XY: 74406

African (AFR) AF: 0.297 AC: 12327 AN: 41480

American (AMR) AF: 0.0833 AC: 1273 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0700 AC: 243 AN: 3470

East Asian (EAS) AF: 0.000770 AC: 4 AN: 5194

South Asian (SAS) AF: 0.0753 AC: 364 AN: 4832

European-Finnish (FIN) AF: 0.125 AC: 1320 AN: 10596

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.124 AC: 8451 AN: 67984

Other (OTH) AF: 0.121 AC: 255 AN: 2116

Alfa AF: 0.206 Hom.: 1023

Bravo AF: 0.162

Asia WGS AF: 0.0460 AC: 160 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.0
DANN	Benign	0.87
PhyloP100		0.096
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: rs1226749; hg19: chr1-45638486;