rs870272

Positions:

• chr9-122191281-C-T

Variant summary

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

The NM_198469.4(MORN5):​c.440-8604C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.427 in 152,138 control chromosomes in the GnomAD database, including 17,518 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 0.43 (17518 hom., cov: 33)
• Consequence: MORN5 NM_198469.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79

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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.607 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MORN5	NM_198469.4	c.440-8604C>T		intron_variant		ENST00000373764.8
MORN5	NM_001286828.2	c.*37-8604C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MORN5	ENST00000373764.8	c.440-8604C>T		intron_variant		1	NM_198469.4	P1
MORN5	ENST00000536616.5	c.*37-8604C>T		intron_variant		1
MORN5	ENST00000486801.1	n.281-8604C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.427 AC: 64948 AN: 152020 Hom.: 17523 Cov.: 33

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.647

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.612

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.427 AC: 64933 AN: 152138 Hom.: 17518 Cov.: 33 AF XY: 0.420 AC XY: 31254 AN XY: 74354

Gnomad4 AFR AF: 0.120

Gnomad4 AMR AF: 0.429

Gnomad4 ASJ AF: 0.531

Gnomad4 EAS AF: 0.106

Gnomad4 SAS AF: 0.518

Gnomad4 FIN AF: 0.487

Gnomad4 NFE AF: 0.612

Gnomad4 OTH AF: 0.462

Alfa AF: 0.578 Hom.: 34984

Bravo AF: 0.405

Asia WGS AF: 0.293 AC: 1023 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.019
DANN	Benign	0.58

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: rs870272; hg19: chr9-124953560; COSMIC: COSV65648970;