dbSNP rs4718067: ZNF736:c.*6871G>A (chr7-64356018-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001170905.3(ZNF736):c.*6871G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 179,716 control chromosomes in the GnomAD database, including 7,898 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 0.31 ( 7369 hom., cov: 32)

Exomes 𝑓: 0.20 ( 529 hom. )

Consequence

ZNF736
NM_001170905.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.33

Publications

2 publications found

Variant links:

Genes affected

ZNF736 (HGNC:32467): (zinc finger protein 736) 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, DNA-templated. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZNF736 links:

TRIM60P18 (HGNC:38490): (tripartite motif containing 60 pseudogene 18)

TRIM60P18 links:

ENSG00000287699 (HGNC:):

ENSG00000287699 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=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.331 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF736	NM_001170905.3 link	c.*6871G>A		3_prime_UTR_variant	Exon 4 of 4	ENST00000423484.3	NP_001164376.1	B4DX44
TRIM60P18		n.64356018G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
ZNF736	ENST00000423484.3 link	c.*6871G>A	3_prime_UTR_variant	Exon 4 of 4	2	NM_001170905.3	ENSP00000400852.1	B4DX44
TRIM60P18	ENST00000441518.1 link	n.647G>A	non_coding_transcript_exon_variant	Exon 2 of 2	6
ENSG00000287699	ENST00000752301.1 link	n.80+15115C>T	intron_variant	Intron 1 of 2
ENSG00000287699	ENST00000752302.1 link	n.50+15115C>T	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.308

AC:

46757

AN:

151902

Hom.:

7364

Cov.:

show subpopulations

Gnomad AFR

AF:

0.336

Gnomad AMI

AF:

0.508

Gnomad AMR

AF:

0.303

Gnomad ASJ

AF:

0.350

Gnomad EAS

AF:

0.247

Gnomad SAS

AF:

0.226

Gnomad FIN

AF:

0.283

Gnomad MID

AF:

0.291

Gnomad NFE

AF:

0.302

Gnomad OTH

AF:

0.298

GnomAD4 exome

AF:

0.203

AC:

5628

AN:

27696

Hom.:

529

Cov.:

AF XY:

0.199

AC XY:

3283

AN XY:

16488

show subpopulations

African (AFR)

AF:

0.217

AC:

136

AN:

628

American (AMR)

AF:

0.229

AC:

945

AN:

4124

Ashkenazi Jewish (ASJ)

AF:

0.256

AC:

114

AN:

446

East Asian (EAS)

AF:

0.163

AC:

308

AN:

1888

South Asian (SAS)

AF:

0.150

AC:

501

AN:

3332

European-Finnish (FIN)

AF:

0.171

AC:

387

AN:

2258

Middle Eastern (MID)

AF:

0.269

AC:

432

AN:

1606

European-Non Finnish (NFE)

AF:

0.211

AC:

2621

AN:

12410

Other (OTH)

AF:

0.183

AC:

184

AN:

1004

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.427

Heterozygous variant carriers

163

326

489

652

815

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

144

216

288

360

<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:

0.308

AC:

46778

AN:

152020

Hom.:

7369

Cov.:

AF XY:

0.306

AC XY:

22765

AN XY:

74286

show subpopulations

African (AFR)

AF:

0.336

AC:

13912

AN:

41446

American (AMR)

AF:

0.302

AC:

4621

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.350

AC:

1213

AN:

3464

East Asian (EAS)

AF:

0.247

AC:

1275

AN:

5168

South Asian (SAS)

AF:

0.225

AC:

1084

AN:

4822

European-Finnish (FIN)

AF:

0.283

AC:

2985

AN:

10552

Middle Eastern (MID)

AF:

0.293

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.302

AC:

20515

AN:

67972

Other (OTH)

AF:

0.297

AC:

625

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1634

3268

4901

6535

8169

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

464

928

1392

1856

2320

<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:

0.310

Hom.:

1189

Bravo

AF:

0.310

Asia WGS

AF:

0.261

AC:

908

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

8.0

(source)

DANN

Benign

0.51

PhyloP100

-1.3

Splicing

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