Variant 8-118783000-A-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The variant allele was found at a frequency of 0.503 in 151,956 control chromosomes in the GnomAD database, including 20,978 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 0.50 ( 20978 hom., cov: 31)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.365

Variant links:

Genes affected

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.712 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.118783000A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
SAMD12-AS1	ENST00000625758.3 linkuse as main transcript	n.1320+18616A>G	intron_variant	5
SAMD12-AS1	ENST00000629661.1 linkuse as main transcript	n.495+56933A>G	intron_variant	5
SAMD12-AS1	ENST00000658340.1 linkuse as main transcript	n.900+18616A>G	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.503

AC:

76318

AN:

151838

Hom.:

20956

Cov.:

show subpopulations

Gnomad AFR

AF:

0.718

Gnomad AMI

AF:

0.285

Gnomad AMR

AF:

0.491

Gnomad ASJ

AF:

0.497

Gnomad EAS

AF:

0.686

Gnomad SAS

AF:

0.591

Gnomad FIN

AF:

0.317

Gnomad MID

AF:

0.434

Gnomad NFE

AF:

0.387

Gnomad OTH

AF:

0.480

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

GnomAD4 genome

AF:

0.503

AC:

76391

AN:

151956

Hom.:

20978

Cov.:

AF XY:

0.502

AC XY:

37244

AN XY:

74252

show subpopulations

Gnomad4 AFR

AF:

0.718

Gnomad4 AMR

AF:

0.490

Gnomad4 ASJ

AF:

0.497

Gnomad4 EAS

AF:

0.686

Gnomad4 SAS

AF:

0.591

Gnomad4 FIN

AF:

0.317

Gnomad4 NFE

AF:

0.387

Gnomad4 OTH

AF:

0.477

Alfa

AF:

0.439

Hom.:

2016

Bravo

AF:

0.522

Asia WGS

AF:

0.607

AC:

2108

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

4.8

DANN

Benign

0.43

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