chr9-122159971-C-T

Position:

• chr9-122159971-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Strong BP6_Moderate BS2

The NM_198469.4(MORN5):​c.-2C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00939 in 1,613,744 control chromosomes in the GnomAD database, including 111 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.0058 (5 hom., cov: 32)
  • Exomes 𝑓: 0.0098 (106 hom.)
• Consequence: MORN5 NM_198469.4 5_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0160

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BP6: Variant 9-122159971-C-T is Benign according to our data. Variant chr9-122159971-C-T is described in ClinVar as [Benign]. Clinvar id is 1879742.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAd4 at 5 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MORN5	NM_198469.4	c.-2C>T		5_prime_UTR_variant	1/5	ENST00000373764.8
MORN5	NM_001286828.2	c.-2C>T		5_prime_UTR_variant	1/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MORN5	ENST00000373764.8	c.-2C>T		5_prime_UTR_variant	1/5	1	NM_198469.4	P1
MORN5	ENST00000536616.5	c.-2C>T		5_prime_UTR_variant	1/4	1

Frequencies

GnomAD3 genomes AF: 0.00579 AC: 881 AN: 152162 Hom.: 5 Cov.: 32

Gnomad AFR AF: 0.00225

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00222

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00248

Gnomad FIN AF: 0.00170

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0106

Gnomad OTH AF: 0.00191

GnomAD3 exomes AF: 0.00594 AC: 1491 AN: 251080 Hom.: 9 AF XY: 0.00583 AC XY: 792 AN XY: 135786

Gnomad AFR exome AF: 0.00222

Gnomad AMR exome AF: 0.00278

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00242

Gnomad FIN exome AF: 0.00370

Gnomad NFE exome AF: 0.0103

Gnomad OTH exome AF: 0.00539

GnomAD4 exome AF: 0.00976 AC: 14265 AN: 1461464 Hom.: 106 Cov.: 31 AF XY: 0.00941 AC XY: 6842 AN XY: 727056

Gnomad4 AFR exome AF: 0.00155

Gnomad4 AMR exome AF: 0.00262

Gnomad4 ASJ exome AF: 0.0000765

Gnomad4 EAS exome AF: 0.0000252

Gnomad4 SAS exome AF: 0.00247

Gnomad4 FIN exome AF: 0.00326

Gnomad4 NFE exome AF: 0.0118

Gnomad4 OTH exome AF: 0.00871

GnomAD4 genome AF: 0.00579 AC: 881 AN: 152280 Hom.: 5 Cov.: 32 AF XY: 0.00520 AC XY: 387 AN XY: 74474

Gnomad4 AFR AF: 0.00224

Gnomad4 AMR AF: 0.00222

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00248

Gnomad4 FIN AF: 0.00170

Gnomad4 NFE AF: 0.0106

Gnomad4 OTH AF: 0.00189

Alfa AF: 0.00769 Hom.: 2

Bravo AF: 0.00574

Asia WGS AF: 0.00173 AC: 6 AN: 3478

EpiCase AF: 0.00851

EpiControl AF: 0.00717

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jan 01, 2023

MORN5: BP4, BS1, BS2 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	9.9
DANN	Benign	0.80

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: rs72767777; hg19: chr9-124922250;