rs16911551

chr9-122188198-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 85 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MORN5	NM_198469.4	c.440-11687C>T		intron_variant		ENST00000373764.8
MORN5	NM_001286828.2	c.*37-11687C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MORN5	ENST00000373764.8	c.440-11687C>T		intron_variant		1	NM_198469.4	P1
MORN5	ENST00000536616.5	c.*37-11687C>T		intron_variant		1
MORN5	ENST00000486801.1	n.281-11687C>T		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.00768

Gnomad4 AMR AF: 0.0186

Gnomad4 ASJ AF: 0.0107

Gnomad4 EAS AF: 0.0328

Gnomad4 SAS AF: 0.0346

Gnomad4 FIN AF: 0.0649

Gnomad4 NFE AF: 0.0421

Gnomad4 OTH AF: 0.0294

Alfa AF: 0.0361 Hom.: 33

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs16911551; hg19: chr9-124950477;