rs2096437

Variant names:

• chr1-45282709-G-A
• rs2096437
• ENST00000464588.1:n.227+21218C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-45282709-G-A
• chr1-45282709-G-T

Variant summary

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

The ENST00000464588.1(ZSWIM5):​n.227+21218C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 152,120 control chromosomes in the GnomAD database, including 3,011 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 (3011 hom., cov: 32)
• Consequence: ZSWIM5 ENST00000464588.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.157

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.335 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZSWIM5	ENST00000464588.1	n.227+21218C>T		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24866 AN: 152002 Hom.: 3012 Cov.: 32

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.0819

Gnomad ASJ AF: 0.0700

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0744

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.164 AC: 24872 AN: 152120 Hom.: 3011 Cov.: 32 AF XY: 0.160 AC XY: 11870 AN XY: 74370

Gnomad4 AFR AF: 0.340

Gnomad4 AMR AF: 0.0818

Gnomad4 ASJ AF: 0.0700

Gnomad4 EAS AF: 0.000772

Gnomad4 SAS AF: 0.0740

Gnomad4 FIN AF: 0.109

Gnomad4 NFE AF: 0.109

Gnomad4 OTH AF: 0.127

Alfa AF: 0.0598 Hom.: 53

Bravo AF: 0.168

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.4
DANN	Benign	0.80

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2096437; hg19: chr1-45748381;