16-770249-G-A

Variant summary

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

The ENST00000543963.5(MSLNL):​c.1833C>T​(p.Asn611Asn) 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

2

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]

Genome browser will be placed here

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
MIR662NR_030384.1 linkuse as main transcriptn.67G>A non_coding_transcript_exon_variant 1/1
MIR662unassigned_transcript_2767 use as main transcriptn.7G>A non_coding_transcript_exon_variant 1/1
MSLNL use as main transcriptn.770249G>A intragenic_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
MSLNLENST00000543963.5 linkuse as main transcriptc.1833C>T p.Asn611Asn synonymous_variant 14/155 ENSP00000441381.1 H0YG18
MIR662ENST00000384847.1 linkuse as main transcriptn.67G>A non_coding_transcript_exon_variant 1/16

Frequencies

GnomAD3 genomes
AF:
0.0513
AC:
7800
AN:
152088
Hom.:
631
Cov.:
34
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.:
0
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.:
34
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:
52
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.

Other links and lift over

dbSNP: rs9745376; hg19: chr16-820249; COSMIC: COSV53499492; COSMIC: COSV53499492; API