rs13157657

Positions:

• chr5-61463020-C-A
• chr5-61463020-C-T

Variant summary

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

The NM_020928.2(ZSWIM6):​c.677-9661C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.376 in 151,886 control chromosomes in the GnomAD database, including 10,895 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 0.38 (10895 hom., cov: 32)
• Consequence: ZSWIM6 NM_020928.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0630

Genes affected

ZSWIM6 (HGNC:29316): (zinc finger SWIM-type containing 6) The protein encoded by this gene contains a zinc finger SWI2/SNF2 and MuDR (SWIM) domain. Proteins with SWIM domains have been found in a diverse number of species and are predicted to interact with DNA or proteins. Mutations in this gene result in acromelic frontonasal dysostosis. [provided by RefSeq, Apr 2017]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.416 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZSWIM6	NM_020928.2	c.677-9661C>A		intron_variant		ENST00000252744.6	NP_065979.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZSWIM6	ENST00000252744.6	c.677-9661C>A		intron_variant		5	NM_020928.2	ENSP00000252744	P1

Frequencies

GnomAD3 genomes AF: 0.376 AC: 57074 AN: 151768 Hom.: 10873 Cov.: 32

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.432

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.376 AC: 57137 AN: 151886 Hom.: 10895 Cov.: 32 AF XY: 0.376 AC XY: 27895 AN XY: 74250

Gnomad4 AFR AF: 0.414

Gnomad4 AMR AF: 0.312

Gnomad4 ASJ AF: 0.346

Gnomad4 EAS AF: 0.198

Gnomad4 SAS AF: 0.431

Gnomad4 FIN AF: 0.372

Gnomad4 NFE AF: 0.378

Gnomad4 OTH AF: 0.385

Alfa AF: 0.368 Hom.: 1300

Bravo AF: 0.370

Asia WGS AF: 0.372 AC: 1294 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.6
DANN	Benign	0.59

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: rs13157657; hg19: chr5-60758847;