Genetic Variant ANAPC1P4:n.1078C>T (chr2-87719965-C-T) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NR_160651.1(ANAPC1P4):n.1013C>T 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 0.000579 in 1,540,796 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0026 ( 9 hom., cov: 22)

Exomes 𝑓: 0.00038 ( 3 hom. )

Consequence

ANAPC1P4
NR_160651.1 non_coding_transcript_exon

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.524

Publications

0 publications found

Variant links:

Genes affected

ANAPC1P4 (HGNC:54710): (ANAPC1 pseudogene 4)

ANAPC1P4 links:

NCAL1 (HGNC:56663): (NK cell activity associated lncRNA 1)

NCAL1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.49).

BP6

Variant 2-87719965-C-T is Benign according to our data. Variant chr2-87719965-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 2651106.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 9 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_160651.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANAPC1P4	NR_160651.1		n.1013C>T		non_coding_transcript_exon	Exon 8 of 15
	NCAL1	NR_186253.1		n.1331C>T		non_coding_transcript_exon	Exon 10 of 15

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
ANAPC1P4	ENST00000427434.2	TSL:6	n.1078C>T	non_coding_transcript_exon	Exon 9 of 15
NCAL1	ENST00000643276.1		n.1448C>T	non_coding_transcript_exon	Exon 11 of 18
NCAL1	ENST00000646855.1		n.1322C>T	non_coding_transcript_exon	Exon 10 of 22

Frequencies

GnomAD3 genomes

AF:

0.00259

AC:

367

AN:

141472

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00905

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00138

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00122

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000198

Gnomad OTH

AF:

0.00105

GnomAD2 exomes

AF:

0.000749

AC:

109

AN:

145462

AF XY:

0.000629

show subpopulations

Gnomad AFR exome

AF:

0.00986

Gnomad AMR exome

AF:

0.000434

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.000169

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000208

Gnomad OTH exome

AF:

0.000712

GnomAD4 exome

AF:

0.000375

AC:

525

AN:

1399214

Hom.:

Cov.:

AF XY:

0.000341

AC XY:

238

AN XY:

696978

show subpopulations

African (AFR)

AF:

0.00743

AC:

228

AN:

30704

American (AMR)

AF:

0.000502

AC:

AN:

43808

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

25198

East Asian (EAS)

AF:

0.000538

AC:

AN:

38998

South Asian (SAS)

AF:

0.000230

AC:

AN:

82550

European-Finnish (FIN)

AF:

0.0000394

AC:

AN:

50746

Middle Eastern (MID)

AF:

0.000929

AC:

AN:

4306

European-Non Finnish (NFE)

AF:

0.000175

AC:

186

AN:

1064866

Other (OTH)

AF:

0.000741

AC:

AN:

58038

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.435

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

100

<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:

0.00259

AC:

367

AN:

141582

Hom.:

Cov.:

AF XY:

0.00244

AC XY:

168

AN XY:

68768

show subpopulations

African (AFR)

AF:

0.00902

AC:

326

AN:

36142

American (AMR)

AF:

0.00138

AC:

AN:

14514

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3322

East Asian (EAS)

AF:

0.00122

AC:

AN:

4918

South Asian (SAS)

AF:

0.00

AC:

AN:

4186

European-Finnish (FIN)

AF:

0.00

AC:

AN:

9898

Middle Eastern (MID)

AF:

0.00

AC:

AN:

282

European-Non Finnish (NFE)

AF:

0.000198

AC:

AN:

65512

Other (OTH)

AF:

0.00104

AC:

AN:

1926

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.555

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome 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

Alfa

AF:

0.000129

Hom.:

Bravo

AF:

0.00294

ClinVar

ClinVar submissions

Significance:Likely benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.49

CADD

Benign

2.7

(source)

DANN

Benign

0.89

PhyloP100

-0.52

Splicing

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over