Variant chr6-31879235-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NR_174947.1(EHMT2-AS1):n.272-1009C>A 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 0.769 in 152,126 control chromosomes in the GnomAD database, including 45,918 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.77 ( 45918 hom., cov: 31)

Consequence

EHMT2-AS1
NR_174947.1 intron, non_coding_transcript

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.69

Variant links:

Genes affected

EHMT2-AS1 (HGNC:39751): (EHMT2 and SLC44A4 antisense RNA 1)

EHMT2-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BP6

Variant 6-31879235-C-A is Benign according to our data. Variant chr6-31879235-C-A is described in ClinVar as [Benign]. Clinvar id is 1283725.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.882 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EHMT2-AS1	NR_174947.1 linkuse as main transcript	n.272-1009C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EHMT2-AS1	ENST00000642849.1 linkuse as main transcript	n.272-1009C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.769

AC:

116911

AN:

152008

Hom.:

45852

Cov.:

show subpopulations

Gnomad AFR

AF:

0.889

Gnomad AMI

AF:

0.688

Gnomad AMR

AF:

0.869

Gnomad ASJ

AF:

0.859

Gnomad EAS

AF:

0.799

Gnomad SAS

AF:

0.877

Gnomad FIN

AF:

0.664

Gnomad MID

AF:

0.905

Gnomad NFE

AF:

0.674

Gnomad OTH

AF:

0.825

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

GnomAD4 genome

AF:

0.769

AC:

117038

AN:

152126

Hom.:

45918

Cov.:

AF XY:

0.773

AC XY:

57495

AN XY:

74366

show subpopulations

Gnomad4 AFR

AF:

0.889

Gnomad4 AMR

AF:

0.869

Gnomad4 ASJ

AF:

0.859

Gnomad4 EAS

AF:

0.800

Gnomad4 SAS

AF:

0.878

Gnomad4 FIN

AF:

0.664

Gnomad4 NFE

AF:

0.674

Gnomad4 OTH

AF:

0.827

Alfa

AF:

0.725

Hom.:

49662

Bravo

AF:

0.790

Asia WGS

AF:

0.886

AC:

3082

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

May 15, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.011

DANN

Benign

0.49

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