rs12050510

Variant names:

• chr15-78892777-A-G
• rs12050510
• ENST00000558893.5:n.968A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000558893.5(MORF4L1):​n.968A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 154,300 control chromosomes in the GnomAD database, including 1,360 homozygotes. 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: 𝑓 0.13 (1338 hom., cov: 33)
  • Exomes 𝑓: 0.13 (22 hom.)
• Consequence: MORF4L1 ENST00000558893.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.169
• Publications: 5 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.252 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MORF4L1	NM_006791.4	c.540+464A>G		intron_variant	Intron 8 of 11	ENST00000426013.7	NP_006782.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MORF4L1	ENST00000426013.7	c.540+464A>G		intron_variant	Intron 8 of 11	1	NM_006791.4	ENSP00000408880.2

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19620 AN: 152126 Hom.: 1338 Cov.: 33

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.176

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.0983

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.137

GnomAD4 exome AF: 0.128 AC: 264 AN: 2056 Hom.: 22 Cov.: 0 AF XY: 0.125 AC XY: 133 AN XY: 1062

African (AFR) AF: 0.167 AC: 4 AN: 24

American (AMR) AF: 0.105 AC: 28 AN: 266

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 16

East Asian (EAS) AF: 0.375 AC: 15 AN: 40

South Asian (SAS) AF: 0.0794 AC: 10 AN: 126

European-Finnish (FIN) AF: 0.150 AC: 6 AN: 40

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.133 AC: 195 AN: 1470

Other (OTH) AF: 0.0833 AC: 6 AN: 72

GnomAD4 genome AF: 0.129 AC: 19620 AN: 152244 Hom.: 1338 Cov.: 33 AF XY: 0.130 AC XY: 9706 AN XY: 74422

African (AFR) AF: 0.118 AC: 4919 AN: 41528

American (AMR) AF: 0.134 AC: 2051 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.118 AC: 411 AN: 3470

East Asian (EAS) AF: 0.263 AC: 1368 AN: 5194

South Asian (SAS) AF: 0.0975 AC: 471 AN: 4830

European-Finnish (FIN) AF: 0.138 AC: 1464 AN: 10596

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.124 AC: 8449 AN: 68014

Other (OTH) AF: 0.138 AC: 293 AN: 2116

Alfa AF: 0.121 Hom.: 235

Bravo AF: 0.131

Asia WGS AF: 0.146 AC: 507 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.3
DANN	Benign	0.57
PhyloP100		0.17
Mutation Taster		=100/0	polymorphism (auto)

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: rs12050510; hg19: chr15-79185119;