NM_020883.2:c.2450-1752C>T

Variant names:

• chr1-45022540-G-A
• rs11809982
• NM_020883.2:c.2450-1752C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020883.2(ZSWIM5):​c.2450-1752C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 152,066 control chromosomes in the GnomAD database, including 4,616 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 0.24 (4616 hom., cov: 31)
• Consequence: ZSWIM5 NM_020883.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.134
• 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZSWIM5	NM_020883.2	c.2450-1752C>T		intron_variant	Intron 11 of 13	ENST00000359600.6	NP_065934.1
ZSWIM5	XM_047426192.1	c.2273-1752C>T		intron_variant	Intron 10 of 12		XP_047282148.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZSWIM5	ENST00000359600.6	c.2450-1752C>T		intron_variant	Intron 11 of 13	1	NM_020883.2	ENSP00000352614.5

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36186 AN: 151948 Hom.: 4611 Cov.: 31

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.194

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.238 AC: 36203 AN: 152066 Hom.: 4616 Cov.: 31 AF XY: 0.239 AC XY: 17730 AN XY: 74336

African (AFR) AF: 0.177 AC: 7363 AN: 41490

American (AMR) AF: 0.331 AC: 5046 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.259 AC: 897 AN: 3464

East Asian (EAS) AF: 0.284 AC: 1467 AN: 5170

South Asian (SAS) AF: 0.257 AC: 1236 AN: 4814

European-Finnish (FIN) AF: 0.229 AC: 2424 AN: 10582

Middle Eastern (MID) AF: 0.199 AC: 58 AN: 292

European-Non Finnish (NFE) AF: 0.249 AC: 16954 AN: 67978

Other (OTH) AF: 0.244 AC: 514 AN: 2108

Alfa AF: 0.247 Hom.: 1003

Bravo AF: 0.243

Asia WGS AF: 0.262 AC: 911 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	9.7
DANN	Benign	0.26
PhyloP100		0.13
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: rs11809982; hg19: chr1-45488212;