rs770131587

Variant names:

• chr16-67875965-C-A
• rs770131587
• NM_014329.5:c.103C>A

Your query was ambiguous. Multiple possible variants found:

• chr16-67875965-C-A
• chr16-67875965-C-G
• chr16-67875965-C-T

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 2P and 3B. PM2 BP4_Moderate BP7

The NM_014329.5(EDC4):​c.103C>A​(p.Arg35Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: EDC4 NM_014329.5 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.703
• Publications: 0 publications found

Genes affected

EDC4 (HGNC:17157): (enhancer of mRNA decapping 4) Predicted to be involved in deadenylation-independent decapping of nuclear-transcribed mRNA. Located in P-body and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.19).
• BP7: Synonymous conserved (PhyloP=0.703 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EDC4	NM_014329.5	c.103C>A	p.Arg35Arg	synonymous_variant	Exon 2 of 29	ENST00000358933.10	NP_055144.3
EDC4	NM_001427345.1	c.103C>A	p.Arg35Arg	synonymous_variant	Exon 2 of 28		NP_001414274.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EDC4	ENST00000358933.10	c.103C>A	p.Arg35Arg	synonymous_variant	Exon 2 of 29	1	NM_014329.5	ENSP00000351811.5
EDC4	ENST00000536072.6	n.108C>A		non_coding_transcript_exon_variant	Exon 2 of 17	2
EDC4	ENST00000572221.5	n.413C>A		non_coding_transcript_exon_variant	Exon 3 of 28	2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.19
CADD	Benign	10
DANN	Benign	0.79
PhyloP100		0.70
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.8

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs770131587; hg19: chr16-67909868;