ENST00000331268.9:c.175C>G

Variant names:

• chr15-78884986-C-G
• rs200340713
• ENST00000331268.9:c.175C>G

Variant summary

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

The ENST00000331268.9(MORF4L1):​c.175C>G​(p.Arg59Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. 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. R59H) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: MORF4L1 ENST00000331268.9 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.44
• Publications: 0 publications found

Genes affected

MORF4L1 (HGNC:16989): (mortality factor 4 like 1) Enables protein N-terminus binding activity. Involved in double-strand break repair via homologous recombination and histone modification. Located in nuclear speck. Part of NuA4 histone acetyltransferase complex and Sin3 complex. [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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000331268.9. 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
	MORF4L1	NM_006791.4	MANE Select	c.156-1155C>G		intron	N/A	NP_006782.1	Q9UBU8-2
	MORF4L1	NM_206839.3		c.175C>G	p.Arg59Gly	missense	Exon 4 of 13	NP_996670.1	Q9UBU8-1
	MORF4L1	NM_001265603.2		c.-109-1155C>G		intron	N/A	NP_001252532.1	Q9UBU8-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MORF4L1	ENST00000331268.9	TSL:1	c.175C>G	p.Arg59Gly	missense	Exon 4 of 13	ENSP00000331310.5	Q9UBU8-1
	MORF4L1	ENST00000426013.7	TSL:1 MANE Select	c.156-1155C>G		intron	N/A	ENSP00000408880.2	Q9UBU8-2
	MORF4L1	ENST00000558893.5	TSL:1	n.201-1155C>G		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.11
BayesDel_addAF	Benign	-0.036	T
BayesDel_noAF	Benign	-0.29
CADD	Benign	23
DANN	Uncertain	1.0
DEOGEN2	Benign	0.20	T
Eigen	Uncertain	0.31
Eigen_PC	Uncertain	0.42
FATHMM_MKL	Uncertain	0.90	D
LIST_S2	Benign	0.73	T
M_CAP	Benign	0.0096	T
MetaRNN	Uncertain	0.51	D
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	0.0	N
PhyloP100		3.4
PrimateAI	Uncertain	0.55	T
PROVEAN	Benign	-0.43	N
REVEL	Benign	0.11
Sift	Benign	0.35	T
Sift4G	Benign	0.24	T
Polyphen		0.87	P
Vest4		0.62
MutPred		0.32		Gain of ubiquitination at K62 (P = 0.0178)
MVP		0.51
MPC		0.66
ClinPred		0.48	T
GERP RS		5.6
Varity_R		0.13
gMVP		0.31

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: rs200340713; hg19: chr15-79177328;