rs752084

Positions:

• chr19-48170687-G-A

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_199341.4(ZSWIM9):​c.-37G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 30)
• Consequence: ZSWIM9 NM_199341.4 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.63

Genes affected

ZSWIM9 (HGNC:34495): (zinc finger SWIM-type containing 9) Predicted to act upstream of or within hematopoietic progenitor cell differentiation. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.31).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZSWIM9	NM_199341.4	c.-37G>A		5_prime_UTR_variant	1/4	ENST00000614654.2	NP_955373.3
ZSWIM9	XM_005259449.4	c.-679G>A		5_prime_UTR_variant	1/4		XP_005259506.1
ZSWIM9	XM_006723204.4	c.-270G>A		5_prime_UTR_variant	1/4		XP_006723267.1
ZSWIM9	XM_006723205.3	c.-33G>A		5_prime_UTR_variant	1/4		XP_006723268.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZSWIM9	ENST00000614654.2	c.-37G>A		5_prime_UTR_variant	1/4	5	NM_199341.4	ENSP00000480314	P2
ZSWIM9	ENST00000328759.11			upstream_gene_variant		1		ENSP00000331363	A2

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.31
CADD	Benign	22
DANN	Uncertain	0.98

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs752084; hg19: chr19-48673944;