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. The variant received -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
• Publications: 2 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.335 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000464588.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZSWIM5	ENST00000464588.1	TSL:3	n.227+21218C>T		intron	N/A

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

African (AFR) AF: 0.340 AC: 14075 AN: 41456

American (AMR) AF: 0.0818 AC: 1250 AN: 15286

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

East Asian (EAS) AF: 0.000772 AC: 4 AN: 5180

South Asian (SAS) AF: 0.0740 AC: 357 AN: 4824

European-Finnish (FIN) AF: 0.109 AC: 1151 AN: 10578

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

European-Non Finnish (NFE) AF: 0.109 AC: 7414 AN: 68010

Other (OTH) AF: 0.127 AC: 267 AN: 2110

Alfa AF: 0.0750 Hom.: 118

Bravo AF: 0.168

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.4
DANN	Benign	0.80
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs2096437; hg19: chr1-45748381;