rs7853089

chr9-122170707-T-G

Variant summary

Our verdict is Benign. Variant got -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

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=-0.97).
• 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/exons	MANE	UniProt
MORN5	NM_198469.4	c.307+951T>G		intron_variant		ENST00000373764.8
MORN5	NM_001286828.2	c.196-3789T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MORN5	ENST00000373764.8	c.307+951T>G		intron_variant		1	NM_198469.4	P1

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

Gnomad4 AFR AF: 0.544

Gnomad4 AMR AF: 0.441

Gnomad4 ASJ AF: 0.518

Gnomad4 EAS AF: 0.107

Gnomad4 SAS AF: 0.385

Gnomad4 FIN AF: 0.546

Gnomad4 NFE AF: 0.546

Gnomad4 OTH AF: 0.491

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

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: rs7853089; hg19: chr9-124932986; COSMIC: COSV65648723;