rs7164529

Variant names:

• chr15-78853456-G-A
• rs7164529
• ENST00000379535.8:c.115+12781G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 18 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=-0.92).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MORF4L1	ENST00000379535.8	c.115+12781G>A		intron_variant	Intron 2 of 12	2		ENSP00000368850.4
MORF4L1	ENST00000559697.5	n.415+5375G>A		intron_variant	Intron 1 of 3	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

African (AFR) AF: 0.297 AC: 12331 AN: 41494

American (AMR) AF: 0.340 AC: 5199 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.351 AC: 1217 AN: 3468

East Asian (EAS) AF: 0.242 AC: 1248 AN: 5166

South Asian (SAS) AF: 0.510 AC: 2455 AN: 4818

European-Finnish (FIN) AF: 0.471 AC: 4990 AN: 10586

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.397 AC: 26984 AN: 67960

Other (OTH) AF: 0.348 AC: 733 AN: 2108

Alfa AF: 0.376 Hom.: 27326

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
PhyloP100		-0.39
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: rs7164529; hg19: chr15-79145798;