Variant chr20-10638641-C-CA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_000214.3(JAG1):c.*856_*857insT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.29 ( 6476 hom., cov: 18)

Exomes 𝑓: 0.28 ( 13 hom. )

Consequence

JAG1
NM_000214.3 3_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.73

Variant links:

Genes affected

JAG1 (HGNC:6188): (jagged canonical Notch ligand 1) The jagged 1 protein encoded by JAG1 is the human homolog of the Drosophilia jagged protein. Human jagged 1 is the ligand for the receptor notch 1, the latter is involved in signaling processes. Mutations that alter the jagged 1 protein cause Alagille syndrome. Jagged 1 signalling through notch 1 has also been shown to play a role in hematopoiesis. [provided by RefSeq, Nov 2019]

JAG1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 20-10638641-C-CA is Benign according to our data. Variant chr20-10638641-C-CA is described in ClinVar as [Benign]. Clinvar id is 337729.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.38 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
JAG1	NM_000214.3 linkuse as main transcript	c.856_857insT		3_prime_UTR_variant	26/26	ENST00000254958.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
JAG1	ENST00000254958.10 linkuse as main transcript	c.856_857insT		3_prime_UTR_variant	26/26	1	NM_000214.3	P1	P78504-1
JAG1	ENST00000423891.6 linkuse as main transcript	n.3550-675_3550-674insT		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes

AF:

0.286

AC:

43532

AN:

151958

Hom.:

6468

Cov.:

show subpopulations

Gnomad AFR

AF:

0.251

Gnomad AMI

AF:

0.511

Gnomad AMR

AF:

0.388

Gnomad ASJ

AF:

0.276

Gnomad EAS

AF:

0.180

Gnomad SAS

AF:

0.218

Gnomad FIN

AF:

0.257

Gnomad MID

AF:

0.288

Gnomad NFE

AF:

0.299

Gnomad OTH

AF:

0.319

GnomAD4 exome

AF:

0.281

AC:

117

AN:

416

Hom.:

Cov.:

AF XY:

0.268

AC XY:

AN XY:

250

show subpopulations

Gnomad4 FIN exome

AF:

0.279

Gnomad4 NFE exome

AF:

0.500

Gnomad4 OTH exome

AF:

0.500

GnomAD4 genome

AF:

0.287

AC:

43577

AN:

152076

Hom.:

6476

Cov.:

AF XY:

0.287

AC XY:

21310

AN XY:

74342

show subpopulations

Gnomad4 AFR

AF:

0.251

Gnomad4 AMR

AF:

0.388

Gnomad4 ASJ

AF:

0.276

Gnomad4 EAS

AF:

0.180

Gnomad4 SAS

AF:

0.218

Gnomad4 FIN

AF:

0.257

Gnomad4 NFE

AF:

0.299

Gnomad4 OTH

AF:

0.320

Alfa

AF:

0.156

Hom.:

293

Bravo

AF:

0.292

Asia WGS

AF:

0.214

AC:

745

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Isolated Nonsyndromic Congenital Heart Disease

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over