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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903535	XR_007064727.1	n.39-563A>T		intron_variant	Intron 1 of 1
LOC124903535	XR_007064726.1	n.-217A>T		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MORF4L1	ENST00000379535.8	c.116-16102A>T		intron_variant	Intron 2 of 12	2		ENSP00000368850.4
MORF4L1	ENST00000559697.5	n.415+14030A>T		intron_variant	Intron 1 of 3	5

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 v4.3

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

Other links and lift over

dbSNP: rs12595538; hg19: chr15-79154453;