chr15-78853456-G-A

Position:

• chr15-78853456-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000379535.8(MORF4L1):​c.115+12781G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.365 in 152,080 control chromosomes in the GnomAD database, including 10,607 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 0.37 (10607 hom., cov: 32)
• Consequence: MORF4L1 ENST00000379535.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.394

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.493 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MORF4L1	ENST00000379535.8	c.115+12781G>A		intron_variant		2		ENSP00000368850
MORF4L1	ENST00000559697.5	n.415+5375G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.365 AC: 55501 AN: 151962 Hom.: 10598 Cov.: 32

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.332

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.365 AC: 55533 AN: 152080 Hom.: 10607 Cov.: 32 AF XY: 0.369 AC XY: 27438 AN XY: 74344

Gnomad4 AFR AF: 0.297

Gnomad4 AMR AF: 0.340

Gnomad4 ASJ AF: 0.351

Gnomad4 EAS AF: 0.242

Gnomad4 SAS AF: 0.510

Gnomad4 FIN AF: 0.471

Gnomad4 NFE AF: 0.397

Gnomad4 OTH AF: 0.348

Alfa AF: 0.382 Hom.: 17704

Bravo AF: 0.347

Asia WGS AF: 0.413 AC: 1436 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.14

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7164529; hg19: chr15-79145798;