Variant rs9745376 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The ENST00000543963.5(MSLNL):c.1833C>T(p.Asn611=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0203 in 529,760 control chromosomes in the GnomAD database, including 815 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 0.051 ( 638 hom., cov: 34)

Exomes 𝑓: 0.0077 ( 177 hom. )

Consequence

MSLNL
ENST00000543963.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.833

Variant links:

Genes affected

MSLNL (HGNC:14170): (mesothelin like) Predicted to be involved in cell-matrix adhesion. Predicted to be located in membrane. Predicted to be integral component of membrane. Predicted to be active in cell surface. [provided by Alliance of Genome Resources, Apr 2022]

MSLNL links:

MIR662 (HGNC:32918): (microRNA 662) microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]

MIR662 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BP7

Synonymous conserved (PhyloP=-0.833 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.172 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR662	NR_030384.1 linkuse as main transcript	n.67G>A		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MSLNL	ENST00000543963.5 linkuse as main transcript	c.1833C>T	p.Asn611=	synonymous_variant	14/15	5		ENSP00000441381	P1
MIR662	ENST00000384847.1 linkuse as main transcript	n.67G>A		mature_miRNA_variant	1/1

Frequencies

GnomAD3 genomes

AF:

0.0513

AC:

7800

AN:

152088

Hom.:

631

Cov.:

show subpopulations

Gnomad AFR

AF:

0.175

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0200

Gnomad ASJ

AF:

0.00144

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.00207

Gnomad FIN

AF:

0.000282

Gnomad MID

AF:

0.0253

Gnomad NFE

AF:

0.00196

Gnomad OTH

AF:

0.0398

GnomAD3 exomes

AF:

0.0141

AC:

3316

AN:

234604

Hom.:

212

AF XY:

0.0103

AC XY:

1328

AN XY:

128506

show subpopulations

Gnomad AFR exome

AF:

0.181

Gnomad AMR exome

AF:

0.00985

Gnomad ASJ exome

AF:

0.00158

Gnomad EAS exome

AF:

0.000389

Gnomad SAS exome

AF:

0.00265

Gnomad FIN exome

AF:

0.000584

Gnomad NFE exome

AF:

0.00186

Gnomad OTH exome

AF:

0.00646

GnomAD4 exome

AF:

0.00774

AC:

2924

AN:

377556

Hom.:

177

Cov.:

AF XY:

0.00598

AC XY:

1287

AN XY:

215072

show subpopulations

Gnomad4 AFR exome

AF:

0.180

Gnomad4 AMR exome

AF:

0.00985

Gnomad4 ASJ exome

AF:

0.00104

Gnomad4 EAS exome

AF:

0.000381

Gnomad4 SAS exome

AF:

0.00274

Gnomad4 FIN exome

AF:

0.000425

Gnomad4 NFE exome

AF:

0.00145

Gnomad4 OTH exome

AF:

0.0101

GnomAD4 genome

AF:

0.0515

AC:

7836

AN:

152204

Hom.:

638

Cov.:

AF XY:

0.0499

AC XY:

3715

AN XY:

74402

show subpopulations

Gnomad4 AFR

AF:

0.176

Gnomad4 AMR

AF:

0.0199

Gnomad4 ASJ

AF:

0.00144

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00207

Gnomad4 FIN

AF:

0.000282

Gnomad4 NFE

AF:

0.00196

Gnomad4 OTH

AF:

0.0393

Alfa

AF:

0.0181

Hom.:

109

Bravo

AF:

0.0587

Asia WGS

AF:

0.0150

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

0.18

DANN

Benign

0.80

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over