chr7-6695778-G-A

Position:

• chr7-6695778-G-A

Variant summary

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

The NM_016265.4(ZNF12):​c.238+1561C>T 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 152,178 control chromosomes in the GnomAD database, including 2,686 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 (2686 hom., cov: 33)
• Consequence: ZNF12 NM_016265.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.956

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]

(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 = 0.297 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF12	NM_016265.4	c.238+1561C>T		intron_variant		ENST00000405858.6
ZNF12	NM_006956.3	c.238+1561C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF12	ENST00000405858.6	c.238+1561C>T		intron_variant		1	NM_016265.4	P1
ZNF12	ENST00000404360.5	c.130+1561C>T		intron_variant		1
	ENST00000366167.2	n.136-12523G>A		intron_variant, non_coding_transcript_variant		4
ZNF12	ENST00000342651.9	c.238+1561C>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25179 AN: 152060 Hom.: 2670 Cov.: 33

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.00366

Gnomad SAS AF: 0.0929

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.166 AC: 25235 AN: 152178 Hom.: 2686 Cov.: 33 AF XY: 0.163 AC XY: 12132 AN XY: 74420

Gnomad4 AFR AF: 0.301

Gnomad4 AMR AF: 0.103

Gnomad4 ASJ AF: 0.141

Gnomad4 EAS AF: 0.00367

Gnomad4 SAS AF: 0.0934

Gnomad4 FIN AF: 0.150

Gnomad4 NFE AF: 0.120

Gnomad4 OTH AF: 0.155

Alfa AF: 0.115 Hom.: 918

Bravo AF: 0.170

Asia WGS AF: 0.0720 AC: 254 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	8.1
DANN	Benign	0.53

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: rs10281898; hg19: chr7-6735409;