rs8032771

Positions:

• chr15-78833717-A-G
• chr15-78833717-A-T

Variant summary

Our verdict is Benign. Variant got -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

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.636 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.-9-6835A>G		intron_variant		2		ENSP00000368850

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

Gnomad4 AFR AF: 0.643

Gnomad4 AMR AF: 0.476

Gnomad4 ASJ AF: 0.478

Gnomad4 EAS AF: 0.449

Gnomad4 SAS AF: 0.632

Gnomad4 FIN AF: 0.612

Gnomad4 NFE AF: 0.508

Gnomad4 OTH AF: 0.509

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8032771; hg19: chr15-79126059;