Genetic Variant :null (chr9-16910679-C-T) – ACMG Classification: Benign (-9 pts)

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4BA1

The variant allele was found at a frequency of 0.411 in 151,946 control chromosomes in the GnomAD database, including 13,951 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 0.41 ( 13951 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.81

Variant links:

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ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.14).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.543 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:

0.411

AC:

62351

AN:

151830

Hom.:

13926

Cov.:

show subpopulations

Gnomad AFR

AF:

0.549

Gnomad AMI

AF:

0.531

Gnomad AMR

AF:

0.530

Gnomad ASJ

AF:

0.394

Gnomad EAS

AF:

0.291

Gnomad SAS

AF:

0.419

Gnomad FIN

AF:

0.289

Gnomad MID

AF:

0.439

Gnomad NFE

AF:

0.326

Gnomad OTH

AF:

0.415

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

GnomAD4 genome

AF:

0.411

AC:

62427

AN:

151946

Hom.:

13951

Cov.:

AF XY:

0.411

AC XY:

30536

AN XY:

74260

show subpopulations

Gnomad4 AFR

AF:

0.549

Gnomad4 AMR

AF:

0.530

Gnomad4 ASJ

AF:

0.394

Gnomad4 EAS

AF:

0.292

Gnomad4 SAS

AF:

0.418

Gnomad4 FIN

AF:

0.289

Gnomad4 NFE

AF:

0.326

Gnomad4 OTH

AF:

0.416

Alfa

AF:

0.371

Hom.:

3824

Bravo

AF:

0.434

Asia WGS

AF:

0.409

AC:

1422

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.14

CADD

Benign

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.

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