15-78818751-C-T

Position:

• chr15-78818751-C-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MORF4L1	ENST00000379535.8	c.-10+7710C>T		intron_variant		2

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;