Variant rs2242071 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBA1

The NR_038437.1(LOC100507443):n.98-7083C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.72 in 780,104 control chromosomes in the GnomAD database, including 204,984 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.72 ( 39520 hom., cov: 32)

Exomes 𝑓: 0.72 ( 165464 hom. )

Consequence

LOC100507443
NR_038437.1 intron, non_coding_transcript

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.628

Variant links:

Genes affected

LOC100507443 (HGNC:):

LOC100507443 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.28).

BP6

Variant 2-208129973-C-T is Benign according to our data. Variant chr2-208129973-C-T is described in ClinVar as [Benign]. Clinvar id is 1291617.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.747 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC100507443	NR_038437.1 linkuse as main transcript	n.98-7083C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.718

AC:

109099

AN:

151982

Hom.:

39478

Cov.:

show subpopulations

Gnomad AFR

AF:

0.718

Gnomad AMI

AF:

0.763

Gnomad AMR

AF:

0.604

Gnomad ASJ

AF:

0.718

Gnomad EAS

AF:

0.536

Gnomad SAS

AF:

0.701

Gnomad FIN

AF:

0.755

Gnomad MID

AF:

0.685

Gnomad NFE

AF:

0.752

Gnomad OTH

AF:

0.710

GnomAD4 exome

AF:

0.721

AC:

452796

AN:

628004

Hom.:

165464

AF XY:

0.723

AC XY:

243845

AN XY:

337154

show subpopulations

Gnomad4 AFR exome

AF:

0.714

Gnomad4 AMR exome

AF:

0.556

Gnomad4 ASJ exome

AF:

0.728

Gnomad4 EAS exome

AF:

0.505

Gnomad4 SAS exome

AF:

0.714

Gnomad4 FIN exome

AF:

0.753

Gnomad4 NFE exome

AF:

0.753

Gnomad4 OTH exome

AF:

0.717

GnomAD4 genome

AF:

0.718

AC:

109198

AN:

152100

Hom.:

39520

Cov.:

AF XY:

0.715

AC XY:

53176

AN XY:

74348

show subpopulations

Gnomad4 AFR

AF:

0.718

Gnomad4 AMR

AF:

0.604

Gnomad4 ASJ

AF:

0.718

Gnomad4 EAS

AF:

0.536

Gnomad4 SAS

AF:

0.702

Gnomad4 FIN

AF:

0.755

Gnomad4 NFE

AF:

0.752

Gnomad4 OTH

AF:

0.711

Alfa

AF:

0.736

Hom.:

42619

Bravo

AF:

0.705

Asia WGS

AF:

0.607

AC:

2114

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 29, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.28

CADD

Benign

DANN

Benign

0.76

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over