6-143899267-C-T

Variant names:

• chr6-143899267-C-T
• rs7764938
• NM_001013623.3:c.489+576C>T

Variant summary

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

The NM_001013623.3(ZC2HC1B):​c.489+576C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 151,840 control chromosomes in the GnomAD database, including 3,373 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 0.20 (3373 hom., cov: 32)
• Consequence: ZC2HC1B NM_001013623.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.441
• Publications: 5 publications found

Genes affected

ZC2HC1B (HGNC:21174): (zinc finger C2HC-type containing 1B) Predicted to enable metal ion binding activity. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000280148 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001013623.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZC2HC1B	NM_001013623.3	MANE Select	c.489+576C>T		intron	N/A	NP_001013645.1	Q5TFG8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZC2HC1B	ENST00000237275.9	TSL:1 MANE Select	c.489+576C>T		intron	N/A	ENSP00000237275.6	Q5TFG8
	ENSG00000280148	ENST00000454207.2	TSL:2	n.*433+576C>T		intron	N/A	ENSP00000400756.2	A0A075B6Q4
	ZC2HC1B	ENST00000539295.3	TSL:1	n.676+576C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31042 AN: 151722 Hom.: 3370 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.201

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.205 AC: 31068 AN: 151840 Hom.: 3373 Cov.: 32 AF XY: 0.209 AC XY: 15493 AN XY: 74238

African (AFR) AF: 0.143 AC: 5934 AN: 41534

American (AMR) AF: 0.292 AC: 4429 AN: 15150

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 493 AN: 3470

East Asian (EAS) AF: 0.152 AC: 785 AN: 5180

South Asian (SAS) AF: 0.253 AC: 1217 AN: 4818

European-Finnish (FIN) AF: 0.227 AC: 2409 AN: 10602

Middle Eastern (MID) AF: 0.195 AC: 57 AN: 292

European-Non Finnish (NFE) AF: 0.222 AC: 15074 AN: 67774

Other (OTH) AF: 0.207 AC: 436 AN: 2110

Alfa AF: 0.216 Hom.: 10908

Bravo AF: 0.200

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.77
DANN	Benign	0.49
PhyloP100		-0.44
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: rs7764938; hg19: chr6-144220404;