rs16911551

Variant names:

• chr9-122188198-C-T
• rs16911551
• NM_198469.4:c.440-11687C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_198469.4(MORN5):​c.440-11687C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0305 in 152,220 control chromosomes in the GnomAD database, including 85 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 0.031 (85 hom., cov: 32)
• Consequence: MORN5 NM_198469.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.206
• 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=-0.9).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0305 (4646/152220) while in subpopulation NFE AF = 0.0421 (2865/68010). AF 95% confidence interval is 0.0408. There are 85 homozygotes in GnomAd4. There are 2374 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 85 Unknown gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MORN5	NM_198469.4	c.440-11687C>T		intron_variant	Intron 4 of 4	ENST00000373764.8	NP_940871.2
MORN5	NM_001286828.2	c.*37-11687C>T		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.440-11687C>T		intron_variant	Intron 4 of 4	1	NM_198469.4	ENSP00000362869.3
MORN5	ENST00000536616.5	c.*37-11687C>T		intron_variant	Intron 3 of 3	1		ENSP00000437483.2
MORN5	ENST00000486801.1	n.281-11687C>T		intron_variant	Intron 2 of 2	2

Frequencies

GnomAD3 genomes AF: 0.0306 AC: 4647 AN: 152102 Hom.: 85 Cov.: 32

Gnomad AFR AF: 0.00770

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.0186

Gnomad ASJ AF: 0.0107

Gnomad EAS AF: 0.0327

Gnomad SAS AF: 0.0346

Gnomad FIN AF: 0.0649

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0421

Gnomad OTH AF: 0.0297

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

GnomAD4 genome AF: 0.0305 AC: 4646 AN: 152220 Hom.: 85 Cov.: 32 AF XY: 0.0319 AC XY: 2374 AN XY: 74426

African (AFR) AF: 0.00768 AC: 319 AN: 41538

American (AMR) AF: 0.0186 AC: 284 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0107 AC: 37 AN: 3470

East Asian (EAS) AF: 0.0328 AC: 170 AN: 5182

South Asian (SAS) AF: 0.0346 AC: 167 AN: 4824

European-Finnish (FIN) AF: 0.0649 AC: 687 AN: 10592

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0421 AC: 2865 AN: 68010

Other (OTH) AF: 0.0294 AC: 62 AN: 2108

Alfa AF: 0.0381 Hom.: 182

Bravo AF: 0.0253

Asia WGS AF: 0.0270 AC: 92 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.8
DANN	Benign	0.57
PhyloP100		0.21
Mutation Taster		=100/0	polymorphism

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: rs16911551; hg19: chr9-124950477;