chr15-78833717-A-G

Variant names:

• chr15-78833717-A-G
• rs8032771
• ENST00000379535.8:c.-9-6835A>G

Variant summary

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

The ENST00000379535.8(MORF4L1):​c.-9-6835A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.55 in 152,020 control chromosomes in the GnomAD database, including 23,480 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 0.55 (23480 hom., cov: 31)
• Consequence: MORF4L1 ENST00000379535.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.330
• Publications: 11 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.636 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.-9-6835A>G		intron	N/A	ENSP00000368850.4

Frequencies

GnomAD3 genomes AF: 0.550 AC: 83555 AN: 151902 Hom.: 23443 Cov.: 31

Gnomad AFR AF: 0.643

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.634

Gnomad FIN AF: 0.612

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.508

Gnomad OTH AF: 0.503

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

GnomAD4 genome AF: 0.550 AC: 83640 AN: 152020 Hom.: 23480 Cov.: 31 AF XY: 0.552 AC XY: 40995 AN XY: 74300

African (AFR) AF: 0.643 AC: 26685 AN: 41506

American (AMR) AF: 0.476 AC: 7270 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.478 AC: 1657 AN: 3468

East Asian (EAS) AF: 0.449 AC: 2318 AN: 5162

South Asian (SAS) AF: 0.632 AC: 3036 AN: 4806

European-Finnish (FIN) AF: 0.612 AC: 6442 AN: 10532

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.508 AC: 34550 AN: 67954

Other (OTH) AF: 0.509 AC: 1073 AN: 2110

Alfa AF: 0.547 Hom.: 2859

Bravo AF: 0.540

Asia WGS AF: 0.561 AC: 1955 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.74
PhyloP100		-0.33
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: rs8032771; hg19: chr15-79126059;