rs605203

chr6-31879235-C-Achr6-31879235-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.69

Genes affected

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

ACMG classification

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	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	n.272-1009C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.769 AC: 116911 AN: 152008 Hom.: 45852 Cov.: 31

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.: 31 AF XY: 0.773 AC XY: 57495 AN XY: 74366

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

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

Other links and lift over

dbSNP: rs605203; hg19: chr6-31847012;