dbSNP rs17229970: MACORIS:n.143+25833T>C (chr10-31681473-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 ENST00000775191.1(MACORIS):n.143+25833T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 152,070 control chromosomes in the GnomAD database, including 2,578 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 0.17 ( 2578 hom., cov: 31)

Consequence

MACORIS
ENST00000775191.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.205

Publications

1 publications found

Variant links:

Genes affected

MACORIS (HGNC:53963): (macrophage enriched lincRNA repressor of IFN-gamma signaling)

MACORIS 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 (AMR) allele frequency at 95% confidence interval = 0.229 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MACORIS	ENST00000775191.1 link	n.143+25833T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.168

AC:

25560

AN:

151952

Hom.:

2579

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0613

Gnomad AMI

AF:

0.230

Gnomad AMR

AF:

0.236

Gnomad ASJ

AF:

0.204

Gnomad EAS

AF:

0.102

Gnomad SAS

AF:

0.101

Gnomad FIN

AF:

0.283

Gnomad MID

AF:

0.108

Gnomad NFE

AF:

0.208

Gnomad OTH

AF:

0.173

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

GnomAD4 genome

AF:

0.168

AC:

25564

AN:

152070

Hom.:

2578

Cov.:

AF XY:

0.171

AC XY:

12687

AN XY:

74332

show subpopulations

African (AFR)

AF:

0.0612

AC:

2540

AN:

41496

American (AMR)

AF:

0.236

AC:

3600

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.204

AC:

708

AN:

3472

East Asian (EAS)

AF:

0.102

AC:

527

AN:

5170

South Asian (SAS)

AF:

0.102

AC:

489

AN:

4812

European-Finnish (FIN)

AF:

0.283

AC:

2989

AN:

10558

Middle Eastern (MID)

AF:

0.105

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.208

AC:

14108

AN:

67966

Other (OTH)

AF:

0.172

AC:

363

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1051

2103

3154

4206

5257

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

282

564

846

1128

1410

<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:

0.194

Hom.:

408

Bravo

AF:

0.163

Asia WGS

AF:

0.119

AC:

415

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

3.7

(source)

DANN

Benign

0.55

PhyloP100

-0.20

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