15-78818751-C-T

Variant names:

• chr15-78818751-C-T
• rs4380028
• ENST00000379535.8:c.-10+7710C>T

Variant summary

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

The ENST00000379535.8(MORF4L1):​c.-10+7710C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.341 in 152,104 control chromosomes in the GnomAD database, including 9,370 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 0.34 (9370 hom., cov: 33)
• Consequence: MORF4L1 ENST00000379535.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0100

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.402 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MORF4L1	ENST00000379535.8	c.-10+7710C>T		intron_variant	Intron 1 of 12	2		ENSP00000368850.4

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51875 AN: 151986 Hom.: 9359 Cov.: 33

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.404

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.399

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.341 AC: 51907 AN: 152104 Hom.: 9370 Cov.: 33 AF XY: 0.340 AC XY: 25303 AN XY: 74358

Gnomad4 AFR AF: 0.224

Gnomad4 AMR AF: 0.410

Gnomad4 ASJ AF: 0.394

Gnomad4 EAS AF: 0.405

Gnomad4 SAS AF: 0.281

Gnomad4 FIN AF: 0.301

Gnomad4 NFE AF: 0.399

Gnomad4 OTH AF: 0.364

Alfa AF: 0.391 Hom.: 26413

Bravo AF: 0.350

Asia WGS AF: 0.318 AC: 1107 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.2
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4380028; hg19: chr15-79111093;