6-31879123-G-A

Position:

• chr6-31879123-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BS1 BS2

The NR_174947.1(EHMT2-AS1):​n.271+1045G>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 0.0419 in 776,524 control chromosomes in the GnomAD database, including 787 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.036 (116 hom., cov: 30)
  • Exomes 𝑓: 0.043 (671 hom.)
• Consequence: EHMT2-AS1 NR_174947.1 intron, non_coding_transcript
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.512

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=-0.89).
• BP6: Variant 6-31879123-G-A is Benign according to our data. Variant chr6-31879123-G-A is described in ClinVar as [Benign]. Clinvar id is 1269640.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.036 (5426/150808) while in subpopulation SAS AF= 0.0536 (250/4660). AF 95% confidence interval is 0.0482. There are 116 homozygotes in gnomad4. There are 2683 alleles in male gnomad4 subpopulation. Median coverage is 30. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 116 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EHMT2-AS1	NR_174947.1	n.271+1045G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EHMT2-AS1	ENST00000642849.1	n.271+1045G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0360 AC: 5418 AN: 150680 Hom.: 115 Cov.: 30

Gnomad AFR AF: 0.0133

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0285

Gnomad ASJ AF: 0.0240

Gnomad EAS AF: 0.0283

Gnomad SAS AF: 0.0541

Gnomad FIN AF: 0.0565

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0487

Gnomad OTH AF: 0.0333

GnomAD4 exome AF: 0.0433 AC: 27118 AN: 625716 Hom.: 671 AF XY: 0.0440 AC XY: 14204 AN XY: 322786

Gnomad4 AFR exome AF: 0.0154

Gnomad4 AMR exome AF: 0.0254

Gnomad4 ASJ exome AF: 0.0252

Gnomad4 EAS exome AF: 0.0310

Gnomad4 SAS exome AF: 0.0491

Gnomad4 FIN exome AF: 0.0559

Gnomad4 NFE exome AF: 0.0458

Gnomad4 OTH exome AF: 0.0384

GnomAD4 genome AF: 0.0360 AC: 5426 AN: 150808 Hom.: 116 Cov.: 30 AF XY: 0.0364 AC XY: 2683 AN XY: 73736

Gnomad4 AFR AF: 0.0133

Gnomad4 AMR AF: 0.0289

Gnomad4 ASJ AF: 0.0240

Gnomad4 EAS AF: 0.0286

Gnomad4 SAS AF: 0.0536

Gnomad4 FIN AF: 0.0565

Gnomad4 NFE AF: 0.0487

Gnomad4 OTH AF: 0.0335

Alfa AF: 0.0373 Hom.: 79

Bravo AF: 0.0314

Asia WGS AF: 0.0460 AC: 160 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 16, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.5
DANN	Benign	0.54

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs114951054; hg19: chr6-31846900;