7-149250419-C-T

Variant names:

• chr7-149250419-C-T
• rs140725635
• NM_012256.4:c.285C>T

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4_Moderate BP6_Moderate BP7 BS2

The NM_012256.4(ZNF212):​c.285C>T​(p.Ala95Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00216 in 1,614,122 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0016 (1 hom., cov: 32)
  • Exomes 𝑓: 0.0022 (5 hom.)
• Consequence: ZNF212 NM_012256.4 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.13
• Publications: 0 publications found

Genes affected

ZNF212 (HGNC:13004): (zinc finger protein 212) This gene belongs to the C2H2-type zinc finger gene family. The zinc finger proteins are involved in gene regulation and development, and are quite conserved throughout evolution. Like this gene product, a third of the zinc finger proteins containing C2H2 fingers also contain the KRAB domain, which has been found to be involved in protein-protein interactions. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.35).
• BP6: Variant 7-149250419-C-T is Benign according to our data. Variant chr7-149250419-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 2658142.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-2.13 with no splicing effect.
• BS2: High Homozygotes in GnomAdExome4 at 5 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_012256.4. 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
	ZNF212	NM_012256.4	MANE Select	c.285C>T	p.Ala95Ala	synonymous	Exon 2 of 5	NP_036388.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF212	ENST00000335870.7	TSL:1 MANE Select	c.285C>T	p.Ala95Ala	synonymous	Exon 2 of 5	ENSP00000338572.2	Q9UDV6
	ZNF212	ENST00000877956.1		c.285C>T	p.Ala95Ala	synonymous	Exon 2 of 5	ENSP00000548015.1
	ZNF212	ENST00000462724.1	TSL:5	n.*381C>T		non_coding_transcript_exon	Exon 2 of 3	ENSP00000418167.1	F2Z3G9

Frequencies

GnomAD3 genomes AF: 0.00162 AC: 247 AN: 152128 Hom.: 1 Cov.: 32

Gnomad AFR AF: 0.000411

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00157

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00311

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00247

Gnomad OTH AF: 0.00239

GnomAD2 exomes AF: 0.00129 AC: 325 AN: 251424 AF XY: 0.00133

Gnomad AFR exome AF: 0.000369

Gnomad AMR exome AF: 0.000549

Gnomad ASJ exome AF: 0.000496

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00226

Gnomad NFE exome AF: 0.00207

Gnomad OTH exome AF: 0.00163

GnomAD4 exome AF: 0.00221 AC: 3232 AN: 1461876 Hom.: 5 Cov.: 31 AF XY: 0.00212 AC XY: 1545 AN XY: 727238

African (AFR) AF: 0.000418 AC: 14 AN: 33480

American (AMR) AF: 0.000604 AC: 27 AN: 44724

Ashkenazi Jewish (ASJ) AF: 0.000574 AC: 15 AN: 26136

East Asian (EAS) AF: 0.00 AC: 0 AN: 39700

South Asian (SAS) AF: 0.0000232 AC: 2 AN: 86258

European-Finnish (FIN) AF: 0.00200 AC: 107 AN: 53420

Middle Eastern (MID) AF: 0.000174 AC: 1 AN: 5754

European-Non Finnish (NFE) AF: 0.00266 AC: 2956 AN: 1112012

Other (OTH) AF: 0.00182 AC: 110 AN: 60392

GnomAD4 genome AF: 0.00162 AC: 247 AN: 152246 Hom.: 1 Cov.: 32 AF XY: 0.00173 AC XY: 129 AN XY: 74466

African (AFR) AF: 0.000409 AC: 17 AN: 41534

American (AMR) AF: 0.00157 AC: 24 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5186

South Asian (SAS) AF: 0.00 AC: 0 AN: 4820

European-Finnish (FIN) AF: 0.00311 AC: 33 AN: 10618

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00247 AC: 168 AN: 68006

Other (OTH) AF: 0.00237 AC: 5 AN: 2110

Alfa AF: 0.00154 Hom.: 0

Bravo AF: 0.00161

EpiCase AF: 0.00185

EpiControl AF: 0.00196

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.35
CADD	Benign	3.2
DANN	Benign	0.79
PhyloP100		-2.1
PromoterAI		-0.029	Neutral
Mutation Taster		=100/0	polymorphism

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: rs140725635; hg19: chr7-148947510;