Variant 14-38608194-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 variant allele was found at a frequency of 0.337 in 152,044 control chromosomes in the GnomAD database, including 8,683 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 0.34 ( 8683 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.878

Variant links:

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ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.0).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.337

AC:

51202

AN:

151926

Hom.:

8672

Cov.:

show subpopulations

Gnomad AFR

AF:

0.323

Gnomad AMI

AF:

0.299

Gnomad AMR

AF:

0.334

Gnomad ASJ

AF:

0.255

Gnomad EAS

AF:

0.465

Gnomad SAS

AF:

0.407

Gnomad FIN

AF:

0.378

Gnomad MID

AF:

0.241

Gnomad NFE

AF:

0.331

Gnomad OTH

AF:

0.313

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

GnomAD4 genome

AF:

0.337

AC:

51249

AN:

152044

Hom.:

8683

Cov.:

AF XY:

0.341

AC XY:

25298

AN XY:

74286

show subpopulations

Gnomad4 AFR

AF:

0.323

Gnomad4 AMR

AF:

0.335

Gnomad4 ASJ

AF:

0.255

Gnomad4 EAS

AF:

0.464

Gnomad4 SAS

AF:

0.408

Gnomad4 FIN

AF:

0.378

Gnomad4 NFE

AF:

0.331

Gnomad4 OTH

AF:

0.316

Alfa

AF:

0.327

Hom.:

16434

Bravo

AF:

0.335

Asia WGS

AF:

0.426

AC:

1479

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

2.1

DANN

Benign

0.19

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