dbSNP rs878998: ADCY10P1:n.1584+906C>T (chr6-41112262-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 ENST00000567255.2(ADCY10P1):n.1584+906C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0961 in 152,172 control chromosomes in the GnomAD database, including 740 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 0.096 ( 740 hom., cov: 32)

Consequence

ADCY10P1
ENST00000567255.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.470

Publications

11 publications found

Variant links:

Genes affected

ADCY10P1 (HGNC:):

ADCY10P1 links:

ADCY10P1 (HGNC:44143): (ADCY10 pseudogene 1)

ADCY10P1 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=-0.9).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADCY10P1	NR_026938.2 link	n.1584+906C>T		intron_variant	Intron 6 of 22

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADCY10P1	ENST00000567255.2 link	n.1584+906C>T		intron_variant	Intron 6 of 22	1
ADCY10P1	ENST00000457653.8 link	n.1004+941C>T		intron_variant	Intron 8 of 23	6

Frequencies

GnomAD3 genomes

AF:

0.0961

AC:

14616

AN:

152054

Hom.:

741

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0885

Gnomad AMI

AF:

0.124

Gnomad AMR

AF:

0.102

Gnomad ASJ

AF:

0.142

Gnomad EAS

AF:

0.00289

Gnomad SAS

AF:

0.0298

Gnomad FIN

AF:

0.0839

Gnomad MID

AF:

0.137

Gnomad NFE

AF:

0.110

Gnomad OTH

AF:

0.105

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.0961

AC:

14623

AN:

152172

Hom.:

740

Cov.:

AF XY:

0.0941

AC XY:

7004

AN XY:

74414

show subpopulations

African (AFR)

AF:

0.0884

AC:

3667

AN:

41502

American (AMR)

AF:

0.102

AC:

1564

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.142

AC:

492

AN:

3472

East Asian (EAS)

AF:

0.00290

AC:

AN:

5174

South Asian (SAS)

AF:

0.0298

AC:

144

AN:

4828

European-Finnish (FIN)

AF:

0.0839

AC:

890

AN:

10604

Middle Eastern (MID)

AF:

0.144

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.110

AC:

7476

AN:

67990

Other (OTH)

AF:

0.104

AC:

220

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

675

1350

2026

2701

3376

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

160

320

480

640

800

<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:

0.112

Hom.:

138

Bravo

AF:

0.0994

Asia WGS

AF:

0.0230

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

6.3

(source)

DANN

Benign

0.59

PhyloP100

0.47

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over