16-780640-T-C

Position:

• chr16-780640-T-C

Variant summary

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

The ENST00000543963.5(MSLNL):​c.102-478A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00255 in 532,066 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0017 (1 hom., cov: 33)
  • Exomes 𝑓: 0.0029 (10 hom.)
• Consequence: MSLNL ENST00000543963.5 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -4.43

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 Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BP6: Variant 16-780640-T-C is Benign according to our data. Variant chr16-780640-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 2645859.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAdExome4 at 10 gene

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.102-478A>G		intron_variant		5		ENSP00000441381	P1

Frequencies

GnomAD3 genomes AF: 0.00174 AC: 261 AN: 149938 Hom.: 1 Cov.: 33

Gnomad AFR AF: 0.000347

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000463

Gnomad ASJ AF: 0.00231

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00255

Gnomad FIN AF: 0.00223

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00288

Gnomad OTH AF: 0.000972

GnomAD3 exomes AF: 0.00220 AC: 547 AN: 249146 Hom.: 5 AF XY: 0.00245 AC XY: 331 AN XY: 135346

Gnomad AFR exome AF: 0.000451

Gnomad AMR exome AF: 0.000435

Gnomad ASJ exome AF: 0.00229

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00261

Gnomad FIN exome AF: 0.00376

Gnomad NFE exome AF: 0.00293

Gnomad OTH exome AF: 0.00165

GnomAD4 exome AF: 0.00286 AC: 1094 AN: 382000 Hom.: 10 Cov.: 0 AF XY: 0.00315 AC XY: 686 AN XY: 217466

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.000415

Gnomad4 ASJ exome AF: 0.00222

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00294

Gnomad4 FIN exome AF: 0.00397

Gnomad4 NFE exome AF: 0.00355

Gnomad4 OTH exome AF: 0.00281

GnomAD4 genome AF: 0.00174 AC: 261 AN: 150066 Hom.: 1 Cov.: 33 AF XY: 0.00167 AC XY: 122 AN XY: 73204

Gnomad4 AFR AF: 0.000346

Gnomad4 AMR AF: 0.000463

Gnomad4 ASJ AF: 0.00231

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00254

Gnomad4 FIN AF: 0.00223

Gnomad4 NFE AF: 0.00288

Gnomad4 OTH AF: 0.000962

Alfa AF: 0.00232 Hom.: 0

Bravo AF: 0.00155

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

Feb 01, 2023

MSLNL: BS2 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	4.2
DANN	Benign	0.91

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs190966078; hg19: chr16-830640;