rs6974325

Variant names:

• chr7-6698852-G-A
• rs6974325
• NM_016265.4:c.16-1041C>T

Your query was ambiguous. Multiple possible variants found:

• chr7-6698852-G-A
• chr7-6698852-G-C
• chr7-6698852-G-T

Variant summary

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

The NM_016265.4(ZNF12):​c.16-1041C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 152,138 control chromosomes in the GnomAD database, including 2,342 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 0.13 (2342 hom., cov: 32)
• Consequence: ZNF12 NM_016265.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.671
• Publications: 5 publications found

Genes affected

ZNF12 (HGNC:12902): (zinc finger protein 12) This gene is a member of the krueppel C2H2-type zinc-finger protein family and encodes a protein with eight C2H2-type zinc fingers and a KRAB domain. This nuclear protein is involved in developmental control of gene expression. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]

ENSG00000228010 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF12	NM_016265.4	c.16-1041C>T		intron_variant	Intron 2 of 4	ENST00000405858.6	NP_057349.2
ZNF12	NM_006956.3	c.16-1041C>T		intron_variant	Intron 2 of 5		NP_008887.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF12	ENST00000405858.6	c.16-1041C>T		intron_variant	Intron 2 of 4	1	NM_016265.4	ENSP00000385939.1

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20339 AN: 152018 Hom.: 2336 Cov.: 32

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.0631

Gnomad EAS AF: 0.275

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.0669

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0450

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.134 AC: 20371 AN: 152138 Hom.: 2342 Cov.: 32 AF XY: 0.136 AC XY: 10134 AN XY: 74390

African (AFR) AF: 0.294 AC: 12185 AN: 41448

American (AMR) AF: 0.115 AC: 1755 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0631 AC: 219 AN: 3470

East Asian (EAS) AF: 0.276 AC: 1426 AN: 5174

South Asian (SAS) AF: 0.156 AC: 752 AN: 4818

European-Finnish (FIN) AF: 0.0669 AC: 709 AN: 10592

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0450 AC: 3059 AN: 68016

Other (OTH) AF: 0.107 AC: 227 AN: 2112

Alfa AF: 0.0517 Hom.: 84

Bravo AF: 0.144

Asia WGS AF: 0.224 AC: 780 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	11
DANN	Benign	0.74
PhyloP100		0.67
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: rs6974325; hg19: chr7-6738483;