9-122180265-A-T

Position:

• chr9-122180265-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_198469.4(MORN5):​c.439+5638A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.476 in 148,120 control chromosomes in the GnomAD database, including 17,454 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 0.48 (17454 hom., cov: 27)
• Consequence: MORN5 NM_198469.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.160

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).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.525 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MORN5	NM_198469.4	c.439+5638A>T		intron_variant		ENST00000373764.8	NP_940871.2
MORN5	NM_001286828.2	c.*36+5638A>T		intron_variant			NP_001273757.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MORN5	ENST00000373764.8	c.439+5638A>T		intron_variant		1	NM_198469.4	ENSP00000362869	P1
MORN5	ENST00000536616.5	c.*36+5638A>T		intron_variant		1		ENSP00000437483
MORN5	ENST00000486801.1	n.280+5638A>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.476 AC: 70430 AN: 148038 Hom.: 17437 Cov.: 27

Gnomad AFR AF: 0.531

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.477

Gnomad MID AF: 0.529

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.454

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

GnomAD4 genome AF: 0.476 AC: 70478 AN: 148120 Hom.: 17454 Cov.: 27 AF XY: 0.470 AC XY: 33715 AN XY: 71774

Gnomad4 AFR AF: 0.531

Gnomad4 AMR AF: 0.394

Gnomad4 ASJ AF: 0.456

Gnomad4 EAS AF: 0.105

Gnomad4 SAS AF: 0.355

Gnomad4 FIN AF: 0.477

Gnomad4 NFE AF: 0.498

Gnomad4 OTH AF: 0.452

Alfa AF: 0.482 Hom.: 2217

Bravo AF: 0.473

Asia WGS AF: 0.269 AC: 937 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	2.1
DANN	Benign	0.85

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: rs7856367; hg19: chr9-124942544; COSMIC: COSV65648759;