NM_003797.5:c.-85G>A

Variant names:

• chr11-86245145-G-A
• rs763617900
• NM_003797.5:c.-85G>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Moderate BP6_Moderate

The NM_003797.5(EED):​c.-85G>A variant causes a 5 prime UTR change. The variant allele was found at a frequency of 0.00000303 in 990,002 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: not found (cov: 30)
  • Exomes 𝑓: 0.0000030 (0 hom.)
• Consequence: EED NM_003797.5 5_prime_UTR
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 6.22
• Publications: 0 publications found

Genes affected

EED (HGNC:3188): (embryonic ectoderm development) This gene encodes a member of the Polycomb-group (PcG) family. PcG family members form multimeric protein complexes, which are involved in maintaining the transcriptional repressive state of genes over successive cell generations. This protein interacts with enhancer of zeste 2, the cytoplasmic tail of integrin beta7, immunodeficiency virus type 1 (HIV-1) MA protein, and histone deacetylase proteins. This protein mediates repression of gene activity through histone deacetylation, and may act as a specific regulator of integrin function. Two transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]

EED Gene-Disease associations (from GenCC):

• Cohen-Gibson syndrome

  Inheritance: AD Classification: STRONG, MODERATE Submitted by: Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae), ClinGen
• Weaver syndrome

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ENSG00000288809 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.32).
• BP6: Variant 11-86245145-G-A is Benign according to our data. Variant chr11-86245145-G-A is described in ClinVar as Likely_benign. ClinVar VariationId is 2642248.Status of the report is criteria_provided_single_submitter, 1 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003797.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EED	NM_003797.5	MANE Select	c.-85G>A		5_prime_UTR	Exon 1 of 12	NP_003788.2
	EED	NM_001308007.2		c.-85G>A		5_prime_UTR	Exon 1 of 13	NP_001294936.1	O75530-2
	EED	NM_001440587.1		c.-85G>A		5_prime_UTR	Exon 1 of 12	NP_001427516.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EED	ENST00000263360.11	TSL:1 MANE Select	c.-85G>A		5_prime_UTR	Exon 1 of 12	ENSP00000263360.6	O75530-1
	EED	ENST00000327320.8	TSL:1	c.-85G>A		5_prime_UTR	Exon 1 of 11	ENSP00000315587.4	O75530-3
	EED	ENST00000673233.3		c.96G>A	p.Ala32Ala	synonymous	Exon 1 of 12	ENSP00000500914.2	A0A5F9ZI63

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome AF: 0.00000303 AC: 3 AN: 990002 Hom.: 0 Cov.: 13 AF XY: 0.00000200 AC XY: 1 AN XY: 500402

African (AFR) AF: 0.00 AC: 0 AN: 20300

American (AMR) AF: 0.00 AC: 0 AN: 23772

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 19116

East Asian (EAS) AF: 0.00 AC: 0 AN: 30684

South Asian (SAS) AF: 0.00 AC: 0 AN: 66624

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 47418

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3540

European-Non Finnish (NFE) AF: 0.00000408 AC: 3 AN: 735426

Other (OTH) AF: 0.00 AC: 0 AN: 43122

GnomAD4 genome Cov.: 30

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.32
CADD	Benign	22
DANN	Benign	0.96
PhyloP100		6.2
PromoterAI		-0.28	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.2

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

Other links and lift over

dbSNP: rs763617900; hg19: chr11-85956187;