15-78862111-A-T

Variant names:

• chr15-78862111-A-T
• rs12595538
• ENST00000379535.8:c.116-16102A>T

Variant summary

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

The ENST00000379535.8(MORF4L1):​c.116-16102A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.361 in 150,826 control chromosomes in the GnomAD database, including 10,165 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 0.36 (10165 hom., cov: 30)
• Consequence: MORF4L1 ENST00000379535.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.504
• Publications: 8 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]

LOC124903535 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.461 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000379535.8. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MORF4L1	ENST00000379535.8	TSL:2	c.116-16102A>T		intron	N/A	ENSP00000368850.4	B3KTM8
	MORF4L1	ENST00000559697.5	TSL:5	n.415+14030A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54468 AN: 150706 Hom.: 10158 Cov.: 30

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.461

Gnomad MID AF: 0.258

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.339

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.361 AC: 54502 AN: 150826 Hom.: 10165 Cov.: 30 AF XY: 0.364 AC XY: 26840 AN XY: 73636

African (AFR) AF: 0.316 AC: 12973 AN: 41094

American (AMR) AF: 0.338 AC: 5117 AN: 15140

Ashkenazi Jewish (ASJ) AF: 0.309 AC: 1070 AN: 3464

East Asian (EAS) AF: 0.232 AC: 1193 AN: 5148

South Asian (SAS) AF: 0.477 AC: 2280 AN: 4778

European-Finnish (FIN) AF: 0.461 AC: 4722 AN: 10244

Middle Eastern (MID) AF: 0.243 AC: 70 AN: 288

European-Non Finnish (NFE) AF: 0.386 AC: 26094 AN: 67672

Other (OTH) AF: 0.344 AC: 720 AN: 2094

Alfa AF: 0.212 Hom.: 543

Bravo AF: 0.347

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.39
DANN	Benign	0.36
PhyloP100		0.50
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12595538;

hg19: chr15-79154453;