rs772105496

Variant names:

• chr16-67875984-A-C
• rs772105496
• NM_014329.5:c.122A>C

Your query was ambiguous. Multiple possible variants found:

• chr16-67875984-A-C
• chr16-67875984-A-G

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_014329.5(EDC4):​c.122A>C​(p.Asn41Thr) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N41S) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: EDC4 NM_014329.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.75
• 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: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EDC4	NM_014329.5	c.122A>C	p.Asn41Thr	missense_variant	Exon 2 of 29	ENST00000358933.10	NP_055144.3
EDC4	NM_001427345.1	c.122A>C	p.Asn41Thr	missense_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.122A>C	p.Asn41Thr	missense_variant	Exon 2 of 29	1	NM_014329.5	ENSP00000351811.5
EDC4	ENST00000536072.6	n.127A>C		non_coding_transcript_exon_variant	Exon 2 of 17	2
EDC4	ENST00000572221.5	n.432A>C		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
AlphaMissense	Benign	0.25
BayesDel_addAF	Uncertain	0.016	T
BayesDel_noAF	Benign	-0.21
CADD	Uncertain	24
DANN	Uncertain	0.99
DEOGEN2	Benign	0.14	T
Eigen	Uncertain	0.45
Eigen_PC	Uncertain	0.54
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Uncertain	0.90	D
M_CAP	Benign	0.0049	T
MetaRNN	Uncertain	0.53	D
MetaSVM	Benign	-0.75	T
MutationAssessor	Uncertain	2.1	M
PhyloP100		6.8
PrimateAI	Uncertain	0.58	T
PROVEAN	Benign	-1.5	N
REVEL	Benign	0.11
Sift	Uncertain	0.010	D
Sift4G	Uncertain	0.0070	D
Polyphen		0.80	P
Vest4		0.70
MutPred		0.30		Gain of sheet (P = 0.0101);
MVP		0.48
MPC		1.4
ClinPred		0.91	D
GERP RS		5.9
Varity_R		0.23
gMVP		0.54

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: rs772105496; hg19: chr16-67909887;