rs10281898

Variant names:

• chr7-6695778-G-A
• rs10281898
• NM_016265.4:c.238+1561C>T

Your query was ambiguous. Multiple possible variants found:

• chr7-6695778-G-A
• chr7-6695778-G-C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 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=-0.87).
• 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 rank	MANE	Protein	UniProt
ZNF12	NM_016265.4	c.238+1561C>T		intron_variant	Intron 4 of 4	ENST00000405858.6	NP_057349.2
ZNF12	NM_006956.3	c.238+1561C>T		intron_variant	Intron 4 of 5		NP_008887.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF12	ENST00000405858.6	c.238+1561C>T		intron_variant	Intron 4 of 4	1	NM_016265.4	ENSP00000385939.1
ZNF12	ENST00000404360.5	c.130+1561C>T		intron_variant	Intron 3 of 4	1		ENSP00000384405.1
ZNF12	ENST00000342651.9	c.238+1561C>T		intron_variant	Intron 4 of 5	2		ENSP00000344745.5
ENSG00000228010	ENST00000366167.2	n.136-12523G>A		intron_variant	Intron 2 of 3	4

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

African (AFR) AF: 0.301 AC: 12481 AN: 41460

American (AMR) AF: 0.103 AC: 1572 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.141 AC: 491 AN: 3472

East Asian (EAS) AF: 0.00367 AC: 19 AN: 5184

South Asian (SAS) AF: 0.0934 AC: 451 AN: 4830

European-Finnish (FIN) AF: 0.150 AC: 1588 AN: 10596

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.120 AC: 8166 AN: 68014

Other (OTH) AF: 0.155 AC: 327 AN: 2114

Alfa AF: 0.130 Hom.: 3529

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
PhyloP100		0.96
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: rs10281898; hg19: chr7-6735409;