rs7853089

Variant names:

• chr9-122170707-T-G
• rs7853089
• NM_198469.4:c.307+951T>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.307+951T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.514 in 152,012 control chromosomes in the GnomAD database, including 20,766 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 0.51 (20766 hom., cov: 32)
• Consequence: MORN5 NM_198469.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16
• Publications: 1 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=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.542 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MORN5	NM_198469.4	c.307+951T>G		intron_variant	Intron 3 of 4	ENST00000373764.8	NP_940871.2
MORN5	NM_001286828.2	c.196-3789T>G		intron_variant	Intron 2 of 3		NP_001273757.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MORN5	ENST00000373764.8	c.307+951T>G		intron_variant	Intron 3 of 4	1	NM_198469.4	ENSP00000362869.3

Frequencies

GnomAD3 genomes AF: 0.514 AC: 78017 AN: 151894 Hom.: 20744 Cov.: 32

Gnomad AFR AF: 0.543

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.442

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.546

Gnomad OTH AF: 0.492

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

GnomAD4 genome AF: 0.514 AC: 78080 AN: 152012 Hom.: 20766 Cov.: 32 AF XY: 0.509 AC XY: 37840 AN XY: 74316

African (AFR) AF: 0.544 AC: 22534 AN: 41446

American (AMR) AF: 0.441 AC: 6738 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.518 AC: 1795 AN: 3466

East Asian (EAS) AF: 0.107 AC: 551 AN: 5162

South Asian (SAS) AF: 0.385 AC: 1853 AN: 4818

European-Finnish (FIN) AF: 0.546 AC: 5773 AN: 10568

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.546 AC: 37128 AN: 67952

Other (OTH) AF: 0.491 AC: 1034 AN: 2108

Alfa AF: 0.513 Hom.: 4179

Bravo AF: 0.503

Asia WGS AF: 0.278 AC: 967 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.38
DANN	Benign	0.74
PhyloP100		-1.2
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: rs7853089; hg19: chr9-124932986; COSMIC: COSV65648723;