Variant 10-86973518-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The XM_047426123.1(LOC124902474):c.305+261G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.599 in 152,042 control chromosomes in the GnomAD database, including 27,817 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 0.60 ( 27817 hom., cov: 32)

Consequence

LOC124902474
XM_047426123.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.539

Variant links:

Genes affected

LOC124902474 (HGNC:):

LOC124902474 links:

ADIRF (HGNC:24043): (adipogenesis regulatory factor) APM2 gene is exclusively expressed in adipose tissue. Its function is currently unknown. [provided by RefSeq, Jul 2008]

ADIRF links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.97).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.899 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124902474	XM_047426123.1 linkuse as main transcript	c.305+261G>A		intron_variant			XP_047282079.1
AGAP11	NR_171046.1 linkuse as main transcript	n.580+2603G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADIRF	ENST00000561504.1 linkuse as main transcript	c.*333+2603G>A		intron_variant, NMD_transcript_variant		3		ENSP00000475582

Frequencies

GnomAD3 genomes

AF:

0.599

AC:

90968

AN:

151924

Hom.:

27788

Cov.:

show subpopulations

Gnomad AFR

AF:

0.514

Gnomad AMI

AF:

0.581

Gnomad AMR

AF:

0.656

Gnomad ASJ

AF:

0.549

Gnomad EAS

AF:

0.921

Gnomad SAS

AF:

0.622

Gnomad FIN

AF:

0.693

Gnomad MID

AF:

0.557

Gnomad NFE

AF:

0.599

Gnomad OTH

AF:

0.611

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

GnomAD4 genome

AF:

0.599

AC:

91052

AN:

152042

Hom.:

27817

Cov.:

AF XY:

0.606

AC XY:

45042

AN XY:

74296

show subpopulations

Gnomad4 AFR

AF:

0.514

Gnomad4 AMR

AF:

0.657

Gnomad4 ASJ

AF:

0.549

Gnomad4 EAS

AF:

0.920

Gnomad4 SAS

AF:

0.622

Gnomad4 FIN

AF:

0.693

Gnomad4 NFE

AF:

0.599

Gnomad4 OTH

AF:

0.614

Alfa

AF:

0.600

Hom.:

3449

Bravo

AF:

0.597

Asia WGS

AF:

0.721

AC:

2510

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

1.2

DANN

Benign

0.24

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over