rs1571586

Variant names:

• chr9-122195246-A-G
• rs1571586
• NM_198469.4:c.440-4639A>G

Variant summary

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

The NM_198469.4(MORN5):​c.440-4639A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.501 in 152,058 control chromosomes in the GnomAD database, including 22,109 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 0.50 (22109 hom., cov: 32)
• Consequence: MORN5 NM_198469.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.165
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.783 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MORN5	NM_198469.4	c.440-4639A>G		intron_variant	Intron 4 of 4	ENST00000373764.8	NP_940871.2
MORN5	NM_001286828.2	c.*37-4639A>G		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.440-4639A>G		intron_variant	Intron 4 of 4	1	NM_198469.4	ENSP00000362869.3
MORN5	ENST00000536616.5	c.*37-4639A>G		intron_variant	Intron 3 of 3	1		ENSP00000437483.2
MORN5	ENST00000486801.1	n.281-4639A>G		intron_variant	Intron 2 of 2	2

Frequencies

GnomAD3 genomes AF: 0.501 AC: 76109 AN: 151940 Hom.: 22059 Cov.: 32

Gnomad AFR AF: 0.790

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.423

Gnomad EAS AF: 0.709

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.468

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

GnomAD4 genome AF: 0.501 AC: 76218 AN: 152058 Hom.: 22109 Cov.: 32 AF XY: 0.505 AC XY: 37525 AN XY: 74328

African (AFR) AF: 0.790 AC: 32759 AN: 41466

American (AMR) AF: 0.508 AC: 7757 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.423 AC: 1464 AN: 3464

East Asian (EAS) AF: 0.709 AC: 3669 AN: 5174

South Asian (SAS) AF: 0.400 AC: 1927 AN: 4820

European-Finnish (FIN) AF: 0.415 AC: 4382 AN: 10562

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.336 AC: 22871 AN: 67976

Other (OTH) AF: 0.470 AC: 992 AN: 2112

Alfa AF: 0.386 Hom.: 49804

Bravo AF: 0.525

Asia WGS AF: 0.573 AC: 1991 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	1.8
DANN	Benign	0.30
PhyloP100		-0.17
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: rs1571586; hg19: chr9-124957525;