dbSNP rs170414: ZNF610:c.-258+54C>T (chr19-52336560-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001161425.2(ZNF610):c.-258+54C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.621 in 157,266 control chromosomes in the GnomAD database, including 30,554 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 0.62 ( 29488 hom., cov: 31)

Exomes 𝑓: 0.63 ( 1066 hom. )

Consequence

ZNF610
NM_001161425.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.283

Publications

2 publications found

Variant links:

Genes affected

ZNF610 (HGNC:26687): (zinc finger protein 610) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZNF610 links:

ENSG00000269535 (HGNC:):

ENSG00000269535 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.644 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF610	NM_001161425.2 link	c.-258+54C>T		intron_variant	Intron 1 of 5	ENST00000403906.8	NP_001154897.1	Q8N9Z0-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF610	ENST00000403906.8 link	c.-258+54C>T		intron_variant	Intron 1 of 5	1	NM_001161425.2	ENSP00000383922.2		Q8N9Z0-1

Frequencies

GnomAD3 genomes

AF:

0.620

AC:

94222

AN:

151880

Hom.:

29479

Cov.:

show subpopulations

Gnomad AFR

AF:

0.651

Gnomad AMI

AF:

0.581

Gnomad AMR

AF:

0.578

Gnomad ASJ

AF:

0.528

Gnomad EAS

AF:

0.421

Gnomad SAS

AF:

0.590

Gnomad FIN

AF:

0.716

Gnomad MID

AF:

0.459

Gnomad NFE

AF:

0.620

Gnomad OTH

AF:

0.603

GnomAD4 exome

AF:

0.634

AC:

3338

AN:

5264

Hom.:

1066

AF XY:

0.619

AC XY:

1836

AN XY:

2966

show subpopulations

African (AFR)

AF:

0.654

AC:

AN:

American (AMR)

AF:

0.583

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.567

AC:

AN:

East Asian (EAS)

AF:

0.318

AC:

AN:

South Asian (SAS)

AF:

0.617

AC:

611

AN:

990

European-Finnish (FIN)

AF:

0.687

AC:

173

AN:

252

Middle Eastern (MID)

AF:

0.450

AC:

AN:

European-Non Finnish (NFE)

AF:

0.639

AC:

2258

AN:

3532

Other (OTH)

AF:

0.641

AC:

205

AN:

320

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

131

197

262

328

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.620

AC:

94274

AN:

152002

Hom.:

29488

Cov.:

AF XY:

0.622

AC XY:

46228

AN XY:

74296

show subpopulations

African (AFR)

AF:

0.650

AC:

26949

AN:

41432

American (AMR)

AF:

0.578

AC:

8820

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.528

AC:

1833

AN:

3470

East Asian (EAS)

AF:

0.422

AC:

2166

AN:

5138

South Asian (SAS)

AF:

0.590

AC:

2846

AN:

4822

European-Finnish (FIN)

AF:

0.716

AC:

7572

AN:

10578

Middle Eastern (MID)

AF:

0.449

AC:

132

AN:

294

European-Non Finnish (NFE)

AF:

0.620

AC:

42162

AN:

67990

Other (OTH)

AF:

0.602

AC:

1265

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1848

3697

5545

7394

9242

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

784

1568

2352

3136

3920

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.626

Hom.:

4427

Bravo

AF:

0.612

Asia WGS

AF:

0.471

AC:

1633

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

6.6

(source)

DANN

Benign

0.77

PhyloP100

-0.28

PromoterAI

0.0097

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over