19-48177727-C-G

Position:

• chr19-48177727-C-G

Variant summary

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

The NM_199341.4(ZSWIM9):​c.276-4728C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 152,110 control chromosomes in the GnomAD database, including 2,320 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 (2320 hom., cov: 32)
• Consequence: ZSWIM9 NM_199341.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZSWIM9	NM_199341.4	c.276-4728C>G		intron_variant		ENST00000614654.2	NP_955373.3
ZSWIM9	XM_005259449.4	c.315-4728C>G		intron_variant			XP_005259506.1
ZSWIM9	XM_006723204.4	c.357-4728C>G		intron_variant			XP_006723267.1
ZSWIM9	XM_006723205.3	c.276-4728C>G		intron_variant			XP_006723268.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZSWIM9	ENST00000614654.2	c.276-4728C>G		intron_variant		5	NM_199341.4	ENSP00000480314	P2
ZSWIM9	ENST00000328759.11	c.276-4728C>G		intron_variant		1		ENSP00000331363	A2

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24611 AN: 151992 Hom.: 2321 Cov.: 32

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.0944

Gnomad FIN AF: 0.0844

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.162 AC: 24628 AN: 152110 Hom.: 2320 Cov.: 32 AF XY: 0.158 AC XY: 11758 AN XY: 74378

Gnomad4 AFR AF: 0.266

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.118

Gnomad4 EAS AF: 0.121

Gnomad4 SAS AF: 0.0940

Gnomad4 FIN AF: 0.0844

Gnomad4 NFE AF: 0.124

Gnomad4 OTH AF: 0.151

Alfa AF: 0.0582 Hom.: 69

Bravo AF: 0.173

Asia WGS AF: 0.120 AC: 415 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.44
DANN	Benign	0.77

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

Publications

LitVar

Other links and lift over

dbSNP: rs10407902; hg19: chr19-48680984;