rs2096437

Positions:

• 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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZSWIM5	ENST00000464588.1	n.227+21218C>T		intron_variant, non_coding_transcript_variant		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;