Genetic Variant NM_001161425.2: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:

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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

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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