NM_004724.4:c.926-197C>A

Variant names:

• chr11-113748617-G-T
• rs7105512
• NM_004724.4:c.926-197C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004724.4(ZW10):​c.926-197C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 151,976 control chromosomes in the GnomAD database, including 2,399 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 (2399 hom., cov: 32)
• Consequence: ZW10 NM_004724.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.91
• Publications: 1 publications found

Genes affected

ZW10 (HGNC:13194): (zw10 kinetochore protein) This gene encodes a protein that is one of many involved in mechanisms to ensure proper chromosome segregation during cell division. This protein is an essential component of the mitotic checkpoint, which prevents cells from prematurely exiting mitosis. [provided by RefSeq, Aug 2011]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZW10	NM_004724.4	c.926-197C>A		intron_variant	Intron 7 of 15	ENST00000200135.8	NP_004715.1
ZW10	XM_017018558.3	c.734-197C>A		intron_variant	Intron 6 of 14		XP_016874047.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZW10	ENST00000200135.8	c.926-197C>A		intron_variant	Intron 7 of 15	1	NM_004724.4	ENSP00000200135.3
ZW10	ENST00000535142.5	n.926-197C>A		intron_variant	Intron 7 of 15	2		ENSP00000440879.1
ZW10	ENST00000538209.1	n.*178-197C>A		intron_variant	Intron 4 of 5	3		ENSP00000439197.1

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26500 AN: 151856 Hom.: 2394 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.0880

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.175

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.175 AC: 26541 AN: 151976 Hom.: 2399 Cov.: 32 AF XY: 0.174 AC XY: 12942 AN XY: 74302

African (AFR) AF: 0.196 AC: 8108 AN: 41440

American (AMR) AF: 0.134 AC: 2050 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.216 AC: 748 AN: 3470

East Asian (EAS) AF: 0.0882 AC: 455 AN: 5158

South Asian (SAS) AF: 0.190 AC: 912 AN: 4808

European-Finnish (FIN) AF: 0.154 AC: 1627 AN: 10556

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.177 AC: 12044 AN: 67980

Other (OTH) AF: 0.187 AC: 395 AN: 2110

Alfa AF: 0.177 Hom.: 1717

Bravo AF: 0.173

Asia WGS AF: 0.139 AC: 484 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.12
DANN	Benign	0.72
PhyloP100		-1.9
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7105512; hg19: chr11-113619339;