Genetic Variant ENST00000562068.2:n.325G>A (chr16-35447822-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The ENST00000562068.2(ZNF971P):n.325G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0266 in 454,902 control chromosomes in the GnomAD database, including 242 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 0.026 ( 64 hom., cov: 34)

Exomes 𝑓: 0.027 ( 178 hom. )

Consequence

ZNF971P
ENST00000562068.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.47

Publications

3 publications found

Variant links:

Genes affected

ZNF971P (HGNC:51848): (zinc finger protein 971, pseudogene)

ZNF971P links:

ENSG00000293007 (HGNC:):

ENSG00000293007 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=-0.72).

BS1

Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0259 (3939/152246) while in subpopulation NFE AF = 0.0401 (2724/68000). AF 95% confidence interval is 0.0388. There are 64 homozygotes in GnomAd4. There are 1863 alleles in the male GnomAd4 subpopulation. Median coverage is 34. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 64 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF971P		n.35447822C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ZNF971P	ENST00000562068.2 link	n.325G>A	non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000293007	ENST00000568619.3 link	n.591G>A	non_coding_transcript_exon_variant	Exon 3 of 3	3
ENSG00000293007	ENST00000720087.1 link	n.357G>A	non_coding_transcript_exon_variant	Exon 3 of 4

Frequencies

GnomAD3 genomes

AF:

0.0259

AC:

3939

AN:

152128

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0108

Gnomad AMI

AF:

0.0351

Gnomad AMR

AF:

0.0160

Gnomad ASJ

AF:

0.0110

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.00331

Gnomad FIN

AF:

0.0363

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.0401

Gnomad OTH

AF:

0.0234

GnomAD2 exomes

AF:

0.0216

AC:

2981

AN:

138018

AF XY:

0.0207

show subpopulations

Gnomad AFR exome

AF:

0.0106

Gnomad AMR exome

AF:

0.0111

Gnomad ASJ exome

AF:

0.0141

Gnomad EAS exome

AF:

0.0000954

Gnomad FIN exome

AF:

0.0370

Gnomad NFE exome

AF:

0.0383

Gnomad OTH exome

AF:

0.0253

GnomAD4 exome

AF:

0.0269

AC:

8141

AN:

302656

Hom.:

178

Cov.:

AF XY:

0.0248

AC XY:

4273

AN XY:

172262

show subpopulations

African (AFR)

AF:

0.0115

AC:

AN:

8590

American (AMR)

AF:

0.0114

AC:

309

AN:

27138

Ashkenazi Jewish (ASJ)

AF:

0.0136

AC:

146

AN:

10730

East Asian (EAS)

AF:

0.00

AC:

AN:

9152

South Asian (SAS)

AF:

0.00304

AC:

181

AN:

59448

European-Finnish (FIN)

AF:

0.0396

AC:

510

AN:

12868

Middle Eastern (MID)

AF:

0.00359

AC:

AN:

2782

European-Non Finnish (NFE)

AF:

0.0412

AC:

6500

AN:

157672

Other (OTH)

AF:

0.0270

AC:

386

AN:

14276

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.462

Heterozygous variant carriers

303

606

910

1213

1516

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

120

<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:

0.0259

AC:

3939

AN:

152246

Hom.:

Cov.:

AF XY:

0.0250

AC XY:

1863

AN XY:

74442

show subpopulations

African (AFR)

AF:

0.0108

AC:

448

AN:

41570

American (AMR)

AF:

0.0160

AC:

245

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.0110

AC:

AN:

3468

East Asian (EAS)

AF:

0.000193

AC:

AN:

5178

South Asian (SAS)

AF:

0.00331

AC:

AN:

4828

European-Finnish (FIN)

AF:

0.0363

AC:

385

AN:

10596

Middle Eastern (MID)

AF:

0.00340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0401

AC:

2724

AN:

68000

Other (OTH)

AF:

0.0232

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.484

Heterozygous variant carriers

190

380

571

761

951

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

126

168

210

<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:

0.0251

Hom.:

Bravo

AF:

0.0238

Asia WGS

AF:

0.00462

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.72

CADD

Benign

4.6

(source)

DANN

Benign

0.61

PhyloP100

1.5

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