rs913935

Variant names:

• chr9-122199025-G-A
• rs913935
• NM_198469.4:c.440-860G>A

Variant summary

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

The NM_198469.4(MORN5):​c.440-860G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.904 in 152,112 control chromosomes in the GnomAD database, including 62,452 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 0.90 (62452 hom., cov: 32)
• Consequence: MORN5 NM_198469.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0680
• Publications: 3 publications found

Genes affected

MORN5 (HGNC:17841): (MORN repeat containing 5)

MORN5 Gene-Disease associations (from GenCC):

• isolated cleft palate

  Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.937 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MORN5	NM_198469.4	c.440-860G>A		intron_variant	Intron 4 of 4	ENST00000373764.8	NP_940871.2
MORN5	NM_001286828.2	c.*37-860G>A		intron_variant	Intron 3 of 3		NP_001273757.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MORN5	ENST00000373764.8	c.440-860G>A		intron_variant	Intron 4 of 4	1	NM_198469.4	ENSP00000362869.3
MORN5	ENST00000536616.5	c.*37-860G>A		intron_variant	Intron 3 of 3	1		ENSP00000437483.2
MORN5	ENST00000486801.1	n.281-860G>A		intron_variant	Intron 2 of 2	2

Frequencies

GnomAD3 genomes AF: 0.904 AC: 137406 AN: 151994 Hom.: 62413 Cov.: 32

Gnomad AFR AF: 0.801

Gnomad AMI AF: 0.970

Gnomad AMR AF: 0.945

Gnomad ASJ AF: 0.931

Gnomad EAS AF: 0.909

Gnomad SAS AF: 0.954

Gnomad FIN AF: 0.948

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.943

Gnomad OTH AF: 0.921

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

GnomAD4 genome AF: 0.904 AC: 137505 AN: 152112 Hom.: 62452 Cov.: 32 AF XY: 0.907 AC XY: 67421 AN XY: 74374

African (AFR) AF: 0.801 AC: 33198 AN: 41438

American (AMR) AF: 0.945 AC: 14464 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.931 AC: 3229 AN: 3470

East Asian (EAS) AF: 0.909 AC: 4702 AN: 5170

South Asian (SAS) AF: 0.953 AC: 4599 AN: 4824

European-Finnish (FIN) AF: 0.948 AC: 10063 AN: 10612

Middle Eastern (MID) AF: 0.952 AC: 280 AN: 294

European-Non Finnish (NFE) AF: 0.943 AC: 64139 AN: 67982

Other (OTH) AF: 0.921 AC: 1948 AN: 2114

Alfa AF: 0.937 Hom.: 38920

Bravo AF: 0.898

Asia WGS AF: 0.943 AC: 3280 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.5
DANN	Benign	0.42
PhyloP100		0.068
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs913935; hg19: chr9-124961304;