16-780767-G-A

Position:

• chr16-780767-G-A

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_Strong BP6_Moderate

The ENST00000543963.5(MSLNL):​c.102-605C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.00019 (0 hom., cov: 25)
  • Exomes 𝑓: 0.000068 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: MSLNL ENST00000543963.5 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -3.08

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]

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BP6: Variant 16-780767-G-A is Benign according to our data. Variant chr16-780767-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2645862.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MSLNL	ENST00000543963.5	c.102-605C>T		intron_variant		5		ENSP00000441381	P1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 17 AN: 91150 Hom.: 0 Cov.: 25 FAILED QC

Gnomad AFR AF: 0.000482

Gnomad AMI AF: 0.00170

Gnomad AMR AF: 0.000109

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000317

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000513

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000607

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.0000658 AC: 15 AN: 228090 Hom.: 0 AF XY: 0.0000483 AC XY: 6 AN XY: 124240

Gnomad AFR exome AF: 0.0000819

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.0000588

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000113

Gnomad OTH exome AF: 0.000183

GnomAD4 exome AF: 0.0000677 AC: 21 AN: 310014 Hom.: 0 Cov.: 0 AF XY: 0.0000457 AC XY: 8 AN XY: 175192

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0000353

Gnomad4 NFE exome AF: 0.000122

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.000186 AC: 17 AN: 91208 Hom.: 0 Cov.: 25 AF XY: 0.000226 AC XY: 10 AN XY: 44304

Gnomad4 AFR AF: 0.000481

Gnomad4 AMR AF: 0.000109

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000317

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000513

Gnomad4 NFE AF: 0.0000607

Gnomad4 OTH AF: 0.00

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

May 01, 2024

MSLNL: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.81
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs200325458; hg19: chr16-830767;