Genetic Variant :null (chr8-78091416-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The variant allele was found at a frequency of 0.464 in 151,664 control chromosomes in the GnomAD database, including 18,301 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 0.46 ( 18301 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.18

Variant links:

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ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.705 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

Frequencies

GnomAD3 genomes

AF:

0.464

AC:

70253

AN:

151546

Hom.:

18262

Cov.:

show subpopulations

Gnomad AFR

AF:

0.712

Gnomad AMI

AF:

0.498

Gnomad AMR

AF:

0.414

Gnomad ASJ

AF:

0.400

Gnomad EAS

AF:

0.504

Gnomad SAS

AF:

0.462

Gnomad FIN

AF:

0.329

Gnomad MID

AF:

0.430

Gnomad NFE

AF:

0.345

Gnomad OTH

AF:

0.447

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

GnomAD4 genome

AF:

0.464

AC:

70344

AN:

151664

Hom.:

18301

Cov.:

AF XY:

0.460

AC XY:

34061

AN XY:

74108

show subpopulations

African (AFR)

AF:

0.712

AC:

29474

AN:

41384

American (AMR)

AF:

0.414

AC:

6285

AN:

15192

Ashkenazi Jewish (ASJ)

AF:

0.400

AC:

1387

AN:

3466

East Asian (EAS)

AF:

0.504

AC:

2582

AN:

5120

South Asian (SAS)

AF:

0.461

AC:

2221

AN:

4814

European-Finnish (FIN)

AF:

0.329

AC:

3462

AN:

10524

Middle Eastern (MID)

AF:

0.435

AC:

128

AN:

294

European-Non Finnish (NFE)

AF:

0.345

AC:

23409

AN:

67856

Other (OTH)

AF:

0.448

AC:

942

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1727

3454

5181

6908

8635

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.412

Hom.:

2444

Bravo

AF:

0.481

Asia WGS

AF:

0.517

AC:

1790

AN:

3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.032

(source)

DANN

Benign

0.60

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.

chr8-78091416-T-C

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over