rs972800

Positions:

• chr19-48186136-T-G

Variant summary

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

The NM_199341.4(ZSWIM9):​c.588+3369T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 152,188 control chromosomes in the GnomAD database, including 4,225 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 0.17 (4225 hom., cov: 33)
• Consequence: ZSWIM9 NM_199341.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.679

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]

CARD8 (HGNC:):

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 = 0.424 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZSWIM9	NM_199341.4	c.588+3369T>G		intron_variant		ENST00000614654.2	NP_955373.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZSWIM9	ENST00000614654.2	c.588+3369T>G		intron_variant		5	NM_199341.4	ENSP00000480314.1
ZSWIM9	ENST00000328759.11	c.588+3369T>G		intron_variant		1		ENSP00000331363.7
CARD8	ENST00000600800.1	n.880+414A>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25250 AN: 152070 Hom.: 4213 Cov.: 33

Gnomad AFR AF: 0.429

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.0891

Gnomad ASJ AF: 0.0729

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.0325

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0498

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.166 AC: 25299 AN: 152188 Hom.: 4225 Cov.: 33 AF XY: 0.164 AC XY: 12230 AN XY: 74434

Gnomad4 AFR AF: 0.429

Gnomad4 AMR AF: 0.0888

Gnomad4 ASJ AF: 0.0729

Gnomad4 EAS AF: 0.160

Gnomad4 SAS AF: 0.178

Gnomad4 FIN AF: 0.0325

Gnomad4 NFE AF: 0.0498

Gnomad4 OTH AF: 0.142

Alfa AF: 0.0741 Hom.: 1157

Bravo AF: 0.182

Asia WGS AF: 0.177 AC: 617 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.6
DANN	Benign	0.59

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs972800; hg19: chr19-48689393;