Genetic Variant ENST00000638208.4:n.2099A>G (chr18-35307950-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000638208.4(ZNF271P):n.2099A>G 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 0.513 in 512,812 control chromosomes in the GnomAD database, including 68,797 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 0.53 ( 21433 hom., cov: 32)

Exomes 𝑓: 0.51 ( 47364 hom. )

Consequence

ZNF271P
ENST00000638208.4 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.70

Publications

16 publications found

Variant links:

COSMIC-nc: COSV67580879

Genes affected

ZNF271P (HGNC:):

ZNF271P links:

ZNF271P (HGNC:13065): (zinc finger protein 271, pseudogene) Zinc finger proteins interact with nucleic acids and have diverse functions. The zinc finger domain is a conserved amino acid sequence motif containing 2 specifically positioned cysteines and 2 histidines that are involved in coordinating zinc. Kruppel-related proteins form 1 family of zinc finger proteins. See ZFP93 (MIM 604749) for additional information on zinc finger proteins.[supplied by OMIM, Apr 2004]

ZNF271P 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=-0.52).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.551 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF271P	NR_024565.1 link	n.2318A>G		non_coding_transcript_exon_variant	Exon 3 of 3
ZNF271P	NR_024566.1 link	n.2095A>G		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ZNF271P	ENST00000638208.4 link	n.2099A>G	non_coding_transcript_exon_variant	Exon 2 of 2	1
ZNF271P	ENST00000399070.4 link	n.2316A>G	non_coding_transcript_exon_variant	Exon 3 of 3	2
ZNF271P	ENST00000639248.1 link	n.2266A>G	non_coding_transcript_exon_variant	Exon 3 of 5	5
ZNF271P	ENST00000465539.3 link	n.*54A>G	downstream_gene_variant		6

Frequencies

GnomAD3 genomes

AF:

0.529

AC:

80353

AN:

151912

Hom.:

21434

Cov.:

show subpopulations

Gnomad AFR

AF:

0.557

Gnomad AMI

AF:

0.449

Gnomad AMR

AF:

0.499

Gnomad ASJ

AF:

0.606

Gnomad EAS

AF:

0.385

Gnomad SAS

AF:

0.493

Gnomad FIN

AF:

0.416

Gnomad MID

AF:

0.646

Gnomad NFE

AF:

0.546

Gnomad OTH

AF:

0.548

GnomAD4 exome

AF:

0.507

AC:

182937

AN:

360782

Hom.:

47364

Cov.:

AF XY:

0.510

AC XY:

104725

AN XY:

205416

show subpopulations

African (AFR)

AF:

0.557

AC:

5577

AN:

10016

American (AMR)

AF:

0.414

AC:

13924

AN:

33646

Ashkenazi Jewish (ASJ)

AF:

0.614

AC:

6730

AN:

10958

East Asian (EAS)

AF:

0.367

AC:

4591

AN:

12510

South Asian (SAS)

AF:

0.495

AC:

31752

AN:

64086

European-Finnish (FIN)

AF:

0.419

AC:

13027

AN:

31088

Middle Eastern (MID)

AF:

0.564

AC:

1568

AN:

2780

European-Non Finnish (NFE)

AF:

0.542

AC:

97585

AN:

179922

Other (OTH)

AF:

0.519

AC:

8183

AN:

15776

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

5067

10134

15202

20269

25336

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

670

1340

2010

2680

3350

<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:

0.529

AC:

80388

AN:

152030

Hom.:

21433

Cov.:

AF XY:

0.522

AC XY:

38787

AN XY:

74294

show subpopulations

African (AFR)

AF:

0.557

AC:

23078

AN:

41466

American (AMR)

AF:

0.498

AC:

7609

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.606

AC:

2103

AN:

3472

East Asian (EAS)

AF:

0.384

AC:

1986

AN:

5168

South Asian (SAS)

AF:

0.492

AC:

2371

AN:

4818

European-Finnish (FIN)

AF:

0.416

AC:

4388

AN:

10556

Middle Eastern (MID)

AF:

0.636

AC:

187

AN:

294

European-Non Finnish (NFE)

AF:

0.546

AC:

37106

AN:

67974

Other (OTH)

AF:

0.546

AC:

1152

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1939

3877

5816

7754

9693

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

708

1416

2124

2832

3540

<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:

0.499

Hom.:

6289

Bravo

AF:

0.536

Asia WGS

AF:

0.402

AC:

1400

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.52

CADD

Benign

9.4

(source)

DANN

Benign

0.78

PhyloP100

1.7

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